Aliases of the Doctor

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Throughout his travels in time and space, the Doctor took and was called by a number of different aliases, titles and names. Some were fleeting. Others, for example John Smith, were used by almost all of his incarnations. The Doctor told few individuals his real name. Instead, he asked others to call him the Doctor.

The Doctor's real name

Ubiquity of the title

"The Doctor" was not a name, but a title. His true name was not generally known, and "the Doctor" became an alias. It has been implied his given name was ceremoniously withdrawn and stricken by his Cousins as punishment for a disgrace he visited upon his House. (PROSE: Lungbarrow)

The Doctor's real name has been said to be difficult to pronounce, for humans at least. He once told an interrogator (when asked his name): "you wouldn't be able to pronounce the first syllable of it." (PROSE: Salvation)

Even when he was twice put on trial by his own people, the Time Lords, he was only referred to as "the Doctor" (TV: The War Games), although the Valeyard, who prosecuted the second trial (and who himself was a culmination of the dark side of a future incarnation of the Doctor) acknowledged that it was an alias. (TV: The Trial of a Time Lord) However, as the Doctor chose that "name" as a Gallifreyan custom (TV: The Sound of Drums), its use in an official capacity is not exceptional. The Doctor kept his true name hidden despite numerous "mind-probe" attempts, voluntary (TV: The Lodger) and involuntary (TV: The Girl in the Fireplace, The Shakespeare Code)

Individuals with knowledge of his name

When the Tenth Doctor first encountered her, River Song claimed to have known him at some point in his future. She was one of the few individuals confirmed to know his true name. To win the Doctor's trust and prove her "credentials", she whispered his name in his ear, and apologised for having to do so. The Doctor seemed shocked at this, later saying to her, "There is only one reason I would ever tell anyone my name, only one time I could." (TV: Forest of the Dead)

She whispered the Doctor's name for a duration of roughly two seconds, suggesting the name may only be a few syllables long (assuming she uttered a complete name). Steven Moffat made a point of mentioning that he always felt the Doctor's name was never revealed only because it must have been some "terrible secret".

When asked about the Sixth Doctor's name, his companion Peri Brown once said that the Doctor had told her she would find it unpronounceable. (AUDIO: Slipback)

The Sixth Doctor told Becky his name. (PROSE: Teach Yourself Ballroom Dancing)

The Eighth Doctor's companion Samantha Jones was told his real name. She found it quite alien and virtually unpronounceable. (PROSE: Unnatural History, Vanderdeken's Children)

When the Doctor spoke his real name aloud in the novel Vanderdeken's Children it was not written in the prose, but represented by "—" instead.

Near the end of his tenth incarnation, members of an unidentified pan-dimensional race came to know the Doctor's real name. At this point he was of the opinion there was no one left in the universe who knew it. (AUDIO: The Last Voyage)

Clara Oswald read his name in The History of the Time War. That time line was later averted however, leaving her with no memory of it. (TV: Journey to the Centre of the TARDIS) Later, when exposed to forces deep within a future version of the dying TARDIS, she began to regain some of those memories. (TV: The Name of the Doctor)

True name

The Carrionite Lilith, unable to discover the Tenth Doctor's true name even with the "witchcraft" used by her kind, remarked, "There is no name. Why would a man hide his title in such despair?" (TV: The Shakespeare Code) The psychically-gifted Evelina, who attempted to foretell the Doctor's future, remarked that his "true name" was "hidden" from her. (TV: The Fires of Pompeii)

The Eleventh Doctor once joked that his middle name was 'Bad Penny', and that he received strange looks when filling in forms. (TV: The God Complex)

According to Dorium Maldovar after his beheading, the religious organisation the Silence had a particular interest in the Doctor's name. He explained that if the Doctor lived long enough, on the fields of Trenzalore, at the fall of the Eleventh, when no creature could speak falsely or fail to answer, a question that must never be answered would be asked: the first question, hidden in plain sight. The question was simply: "Doctor Who?". The Silence wanted to stop the Doctor from revealing his true name. (TV: The Wedding of River Song) The Doctor was at a later time forced to go to Trenzalore to rescue his friends from the Great Intelligence, which sought to gain access to the Doctor's tomb. The tomb, which was a future version of his own dying TARDIS, would open only to the Doctor's real name. Threatening to kill the Doctor's friends if he did not speak his name and open the tomb, the situation was resolved when the data ghost of River Song was able to silently transmit his name to the TARDIS, thus opening the door for the Great Intelligence. (TV: The Name of the Doctor )

Eventually, the Doctor held a book called The History of the Time War in his TARDIS library, unfolding the history of the Last Great Time War and apparently, containing his name. (TV: Journey to the Centre of the TARDIS)

Significance

The Eleventh Doctor told Clara Oswald that his real name was not so important, since he specifically chose in its place the title of "Doctor", "like a promise you make." (TV: The Name of the Doctor) This promise was, as the Tenth and War Doctors recited together, "Never cruel or cowardly. Never give up, never give in." (TV: The Day of the Doctor)

The Saxon Master knew of this and implied that the Doctor's title had been chosen because it meant "the man who makes people better", although he found the choice "sanctimonious" for some one who ended millions of lives and ruined many others. (TV: The Sound of Drums) River Song was aware of this contradiction in the Doctor's behaviour: she said that the Doctor was the first to have this title and that the rest of the universe later adopted it, usually to mean 'healer' or 'wise man'; however, she added, in some parts of the universe (eg. the Gamma Forests), it eventually came to mean 'mighty warrior'. (TV: A Good Man Goes to War)

Far from being a randomly chosen title or one intended to inflate his credentials, the Doctor did possess at least one doctorate. (TV: The Moonbase, The Armageddon Factor, The Mysterious Planet) He sometimes described himself as a "Doctor of many things" (TV: Four to Doomsday) or "everything". (TV: Utopia) Exactly what his doctorate(s) were for remain a mystery, but on several occasions the Doctor stated he was not a medical doctor. (TV: "The Forest of Fear", "Mighty Kublai Khan", AUDIO: Red Dawn) That didn't stop his second, third, tenth and eleventh incarnations from sporting a stethoscope on occasion. (TV: The Runaway Bride, Partners in Crime, Planet of the Ood, Planet of the Dead, The Doctor's Daughter, The Lodger, etc) The Doctor did note that by his second incarnation, he had studied medicine in the 19th century. (TV: The Moonbase) He also claimed one of his doctorates was in cheese making. (TV: The God Complex)

Common aliases

During his life, numerous names, titles and epiphets were either used by or bestowed upon the Time Lord most widely known as the Doctor.

The Doctor

As noted above, the Doctor itself was an alias, despite it being the title by which the Time Lord was most widely known. It has been claimed that, as a Gallifreyan custom, he chose this alias himself. (TV: The Sound of Drums) On one occasion, a human knew this name without the Doctor saying it out loud. (PROSE: Cat's Cradle: Warhead) His other aliases often included the title "Doctor". (TV: Spearhead from Space) He implied to Peri his given name also began with such a title. (TV: The Mysterious Planet) Drax, a fellow Time Lord, indicated the Doctor did indeed possess a doctorate (although in what was not indicated). (TV: The Armageddon Factor) According to one account, during his first incarnation, the Doctor adopted this name in dealing with human colonists on the planet Iwa at the same time that his granddaughter adopted the name "Susan". (PROSE: Frayed) According to another account, the Doctor and Susan already went by these names when they left Gallifrey. (AUDIO: The Beginning)

During his eleventh incarnation, the Doctor claimed that he didn't actually know why he and other people called him 'the Doctor'. (TV: The Lodger)

John Smith

John Smith was an alias the Doctor would frequently use on Earth and around humans when a "standard" name was needed. It was often preceded by the title "Doctor", though not always - for example, when he was undercover as a teacher at a school or a patient in a hospital. (TV: School Reunion, Smith and Jones) The earliest known use occurred during his first incarnation, when he used a library card with the name Dr. J. Smith while living at 76 Totter's Lane, (TV: The Vampires of Venice) as well as for identification when renting the junkyard. (PROSE: The Rag and Bone Man's Story) The inspiration for the alias was John Smith of John Smith and the Common Men, which he was familiar with through Susan. (PROSE: The Witch Hunters) In his second incarnation, the name was independently used by his companion Jamie McCrimmon (who would not have known of the Doctor's earlier use of the name) while the Doctor was being treated for concussion, as he saw it being used as a brand name on a metal container. (TV: The Wheel in Space) Later, he adopted it on a semi-regular basis during his third incarnation while exiled on Earth, when he served as unpaid scientific advisor to UNIT. (TV: Spearhead from Space, et al)

As "John Smith" was considered a generic name in some Earth cultures, the Doctor's use of the alias was occasionally treated with scepticism. (TV: Midnight)

The Doctor twice changed himself into a human who used the name John Smith. This occurred in his seventh incarnation (PROSE: Human Nature) and in his tenth (TV: Human Nature/The Family of Blood).

Known uses of John Smith

On the First Doctor's library card while living at 76 Totter's Lane (TV: The Vampires of Venice)
As identification when renting the junkyard from its owner, Hawkins (PROSE: The Rag and Bone Man's Story)
When Rebecca Nurse asked his name, realising that a simple 'Doctor' would not do (PROSE: The Witch Hunters)
To check in at Ingersoll's tavern in Salem (PROSE: The Witch Hunters).
Given to him by Jamie and used aboard Space Station W3. (TV: The Wheel in Space)
When questioned by a German soldier, who replies "Good. Now we are getting somewhere". (TV: The War Games)
During his exile on Earth with UNIT, when he served as its scientific advisor (TV: Spearhead from Space, Inferno, The Time Warrior)
On the planet Kastopheria when asked by Admiminstrator Charteris, who reponded with "A large family, the Smiths" (PROSE: Catastrophea)
"JSMITH" was the Sixth Doctor's username online (PROSE: Blue Box) and "Jsmith8" was the Eighth's (PROSE: Lonely)
A German variation of this name, "Johann Schmidt," was used by the Sixth Doctor when he infiltrated the Third Reich to investigate the origins of the Fourth Reich that was currently active in 2001, creating fake credentials establishing him as Major-General Johann Schmidt of the Berlin Fifth Medical Corps (PROSE: The Shadow in the Glass). The Seventh Doctor also used this name while impersonating the Reichsinspektor General (PROSE: Timewyrm: Exodus), while the Eighth Doctor used it while posing as a German spy. (AUDIO: Storm Warning) An alternative version of the Eighth Doctor who existed in a timeline where the Nazis won World War II, also used the name. (AUDIO: Colditz, Klein's Story) The Eleventh Doctor took the place of a real Dr. Schmidt when his psychic paper displayed the credentials of a visitor expected at the Lexington Bank. (PROSE: Borrowed Time)
A French variation, "Jean Forgeron," was used by the Fourth Doctor when met by French soldiers in the labyrinth underneath Paris. (COMIC: The Forgotten)
Given to him coincidentally by Chang Lee on his hospital admittance forms after he was shot near the end of his seventh incarnation. (TV: Doctor Who)
Appeared as "Dr. John Smith" on a piece of psychic paper during a visit to 1941 (although he never actually used the alias on this occasion). (TV: The Empty Child)
While working undercover as a science teacher at Deffry Vale High School. (TV: School Reunion)
While posing as a patient at Royal Hope Hospital. (TV: Smith and Jones)
On both the Confederate and Union sides of the American Civil War as a guise under which the Fifth Doctor could render medical assistance, while having the freedom to search for his lost companions, Peri and Erimem. He received some local publicity under the name after delivering the baby of the mayor of Gable, West Virginia. He was personally known to Abraham Lincoln by this name after he had saved the president's life during an assassination attempt in Richmond, Virginia. (PROSE: Blood and Hope)
While impersonating a health and safety officer during an investigation of Adipose Industries. (TV: Partners in Crime)
The Tenth Doctor attempted to use the alias aboard the Crusader 50 bus on the planet Midnight, but it was recognised as a false name and rejected by the panicking humans aboard. (TV: Midnight)
When "reintroducing" himself to Donna Noble after he erased her memories of him. (TV: Journey's End)
When encountering Jackson Lake, a man who, due to Infostamp exposure, believed himself to be an incarnation of the Doctor. (TV: The Next Doctor)
While posing as his Ganger counterpart as an independent name for himself. (TV: The Almost People)
While at Eddison Manor after the murder of Professor Gerald Peach, it was suggested that the police be brought in to investigate the murder. The Doctor, not wanting to get the police involved in a potentially alien crime, replies "Don't have to. Chief Inspector Smith from Scotland Yard." (TV: The Unicorn and the Wasp)
The Doctor introduced himself as Mr Smith, and Clara as his wife. (TV: The Crimson Horror)

Theta Sigma

Theta Sigma (ΘΣ), informally Thete, was a nickname of the Doctor at the Time Lord Academy on Gallifrey. (TV: The Armageddon Factor, The Happiness Patrol, COMIC: Flashback)

In an alternative timeline in which Rassilon failed to finish the Eye of Harmony before his death, the Doctor never left Gallifrey and became a commentator rather than a renegade Time Lord. He was known as Commentator Theta Sigma. (AUDIO: Forever)

Theta Sigma is also seen in River Song's message to the Doctor on the Universe's oldest cliff-face. (TV: The Pandorica Opens)

Doctor Who

The name Doctor Who was applied to the Doctor, intentionally or unintentionally, on many occasions.

The computer WOTAN once referred to the Doctor as Doctor Who, for reasons which have never been explained. (TV: The War Machines)
K9 was heard on occasion making playful remarks related to the Who name. (TV: A Girl's Best Friend, TV: Invasion of the Bane)
The Third Doctor wrote a series of children's books during his time with UNIT which were mistakenly published under this name. (AUDIO: The Kingmaker)

The name was often unintentionally invoked when characters wished to learn who the Doctor was and what his name was: "Doctor? Doctor who?" Often this is done for comic effect; see The "Doctor Who?" running joke.

Other Aliases

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Please help by adding some more information.

A list of aliases used by the Doctor in each of his incarnations.

First Doctor

Doctor Foreman: Often addressed as such due to the assumption that he shared Susan's surname. (TV: An Unearthly Child) Officially used the alias during his the trial for the killing of a werewolf. (PROSE: The Juror's Story)
Maximus Pettulian: While visiting the Roman Empire shortly before the Great Fire of Rome in July 64, the Doctor briefly impersonated a murdered lyre player named Maximus Pettulian in the court of Nero until his true identity was uncovered. (TV: The Romans)
Zeus: When the Greek warrior Achilles mistook the Doctor for Zeus posing as an old man in circa 1200 BC, he went along with it, until the unconvinced Agamemnon spoiled the Doctor's ruse. (TV: The Myth Makers)
Doctor Caligari: The Doctor used it when he arrived in Tombstone, Arizona in October 1881, impersonating a magician. However, the locals mistook him for Doc Holliday. (TV: The Gunfighters)
Benjamin Jackson: Used when he returned to the Salem Village.
Wissfornjarl: While on the Isle of Hoy, Orkney in 1956, the Doctor was given this name by the spaywife Janet McKay. After seeing his arrival in the TARDIS, she mistook him for the island's protector from Norse mythology. He believed that it was simplest to accept the name. The name meant "Wise Old Chieftain," which Ian thought was appropriate. (AUDIO: The Revenants)

Second Doctor

The Examiner: Still not sure if he was the Doctor after his first regeneration, the Doctor took on the identity of an Examiner from Earth after the original one was assassinated by Bragen. (TV: The Power of the Daleks) Near the end of his life, he masquaded as another examiner, this time of a none-existing War Prison in an attempt to liberate Jamie from said prison. (TV: The War Games)
Doktor von Wer: The German translation of 'Doctor [of] Who.' The Second Doctor briefly used this during his visit to Scotland on 16 April 1746. He also signed a note Doctor W around this time. (TV: The Highlanders)
Doctor Galloway: Edward Waterfield made up this name for the Second Doctor when arranging to meet him. (TV: The Evil of the Daleks)
Doctor Mason: An alias used when he took part in a jury at the trial of the First Doctor for killing a werewolf. (PROSE: The Juror's Story)
Dr. Rip Van Winkle: A name given to him by Mrs Craig. (PROSE: The Indestructible Man)
Gaius Iunius Faber: "Iunius Faber" being the Latin equivalent of John Smith. The Second Doctor used this alias during his visit to Bruttium, Italy in 71 BC. (PROSE: The Slave War)

Third Doctor

The Great Wizard, Qui Quae Quod: Miss Hawthorne referred to the Doctor as "the great wizard Quiquaequod" while attempting to bluff the villagers of Devil's End into releasing him. (TV: The Dæmons)

This is actually the masculine, feminine, and neuter nominative forms of the relative pronoun "who", in Latin.

Prisoner 177781: The Doctor was recorded by this designation when he was briefly arrested by the British Army alongside Sarah Jane Smith, who was recorded as Prisoner 177782. (TV: Invasion of the Dinosaurs)
The Master: Forced to masquerade as the Master when the latter switched bodies with him. (PROSE: The Switching)
Doctor Noble: An alias used when he took part in a jury at the trial of the First Doctor for killing a werewolf. (PROSE: The Juror's Story)

Fourth Doctor

Hieronymous: Stole Hieronymous's robes and pretended to be him to defeat the Mandragora Helix. (TV: The Masque of Mandragora)
?: The Doctor signed a document with a question mark prior to the Sontaran invasion of Gallifrey. (TV: The Invasion of Time)

Fifth Doctor

The Supremo: The Doctor called himself "the Supremo" while leading the alliance against the army of the renegade Time Lord Morbius. Originally, his title was "Supreme Controller", but the Ogrons of his personal guard could not pronounce it and shortened it to the simpler "Supremo". (PROSE: Warmonger)
Dr Jonas Smythe: The Doctor used this name when working with Liz Shaw in Italy. (PROSE: Flashpoint)
Doctor Walters: The Doctor used this name while stuck in Victorian London without his TARDIS for a year from November 1866 - 1867. (AUDIO: The Haunting of Thomas Brewster)

Sixth Doctor

Doktor of TARDIS: Used by the Sixth Doctor to move discreetly around an alternate version of the city of Rome. (PROSE: State of Change)
Albert Einstein: Used by the Doctor while meeting with Charles Darwin in the Galapagos Islands in 1835. (AUDIO: Bloodtide)
Banto Zame: Posed as Zame when the latter impersonation of the Doctor landed in him trouble. (AUDIO: The One Doctor)
The Sandman: Adopted as part of a plan to stop an alien race attacking others by inspiring the idea of him as a monster. (AUDIO: The Sandman)
Zarl: After the Doctor had chased him to his death, the Doctor impersonated Zarl to maintain the web of time and his previous incarnation's meeting with Zarl. (AUDIO: Peri and the Piscon Paradox)
Claudius Dark: Used while the Doctor was undercover in the 19th century, so as to avoid the attention of Mr Kempston and Mr Hardwick. (AUDIO: The Hourglass Killers)
Dr. Grigori Kalashnikov: The Doctor adopted the identity of a Moscow University scientist when he arrived at the Baikonur Cosmodrome in Kazakhstan on 10 November 1963. (AUDIO: 1963: The Space Race)

Seventh Doctor

?: The Doctor signed a document with a question mark during a visit to London in 1963. (TV: Remembrance of the Daleks)
Merlin: The Doctor was mistaken by the people from an alternate universe which inspired the Arthurian legend to be Merlin, (TV: Battlefield) due to the Eighth Doctor using the alias when delivering King Arthur. (PROSE: One Fateful Knight)
John Doe: The customary name in America for an unidentified human male was applied to the apparently dead Doctor by the staff of Walker General Hospital, and he was given a "John Doe" toe tag before being wheeled into the morgue's freezer, where he subsequently regenerated into his eighth incarnation. (TV: Doctor Who)
Commander John Ballard: The Doctor was mistaken for the new commander of Dark Space 8 after he and Melanie Bush were teleported aboard the station following the destruction of Ballard's shuttle. (AUDIO: Bang-Bang-A-Boom!)
Mr. Ashcroft: The Doctor used this name to acquire recordings from Bianca's. (AUDIO: The Wormery)
Richard A. Fells: The Doctor used this name while posing as a prisoner in Alcatraz. (PROSE: Inmate 280)
Dr Vaughn Sutton: Used on Perfugium. (AUDIO: Master)
John Rutherford: Using this pseudonym, the Doctor was elected as an independent member of Parliament in May 1963 on a platform of nuclear disarmament. (AUDIO: The Assassination Games)

Eighth Doctor

Dr James Alistair Bowman: Dr. Grace Holloway came up with this name for the Eighth Doctor whilst introducing him to others. (TV: Doctor Who) The Doctor subsequently used this alias on occasion, filling it out to James Alistair Bowman. (PROSE: Seeing I)
The Eight Man Bound: The Doctor referred to himself as this name, based on the fact that the Doctor was the only student to see a glimpse of his future right up to his eight incarnation in the Eighth Man Bound game. (PROSE: Christmas on a Rational Planet, Lungbarrow, The Dying Days)
Gracie Witherspoon: To defeat the Threshold, the Doctor used a personal chameleon circuit to take the appearance of a female Threshold agent while Shayde masqueraded as the Doctor. (COMIC: Wormwood)
The Bringer of Darkness, the Oncoming Storm and the Evergreen Man: all epithets he offered Slake. He also gave his full, former Time Lord title as President of the High Council of the Time Lords, Keeper of the Legacy of Rassilon, Defender of the Laws of Time and Protector of Gallifrey. (PROSE: Vampire Science)
Merlin: Whilst stuck in the otherworld of Avalon, the Doctor attempted to pass himself off as Merlin to Queen Mab. (PROSE: The Shadows of Avalon) He later took up the alias again to deliver King Arthur in another reality. (PROSE: One Fateful Knight)
Dr Friedlander: While visiting Banquo Manor (There was a real Doctor Friedlander who hadn't arrived at the Manor; the Doctor simply assumed the name to avoid having to explain his presence). (PROSE: The Banquo Legacy)
Sir Doctor Peter Pollard: when he arrived at Sebastian Grayle's 19th centuary manor house, with Charllote Pollard pretending to be his daughter. (AUDIO: Seasons of Fear)
Perdix: while in Rhadamanthys' court. (PROSE: Fallen Gods)

War Doctor

The Renegade: A name the Time Lords used to refer to the War Doctor as he planned to use the Moment to end the Last Great Time War. (COMIC: Sky Jacks)
Granddad: A nickname given to him by the Eleventh Doctor while being arrested by Queen Elizabeth I's soldiers in 1562. (TV : The Day of the Doctor)

Ninth Doctor

Mr Spock: Rose Tyler, annoyed with the Doctor not telling her his name, introduced him to Captain Jack as Mr. Spock. (TV: The Empty Child)
Hal Gryden: While on the planet Arkannis Major, the Doctor adopted the name of this fictional newscaster to broadcast a message of peace to the people of the world. (PROSE: The Stealers of Dreams)
Brigadier Bambera: Used when visiting the Christmas truce of World War I. (COMIC: The Forgotten)
Inspector George Dixon: Used when helping the police department on 23rd century New Vegas with their investigation into the Whisper. (AUDIO: Night of the Whisper)

Tenth Doctor

Doctor James McCrimmon: The Tenth Doctor briefly called himself Dr. James McCrimmon while visiting Scotland in 1879; this was the name of one of his old companions. Later, he dropped the alias and was knighted by Queen Victoria as "Sir Doctor of TARDIS". (TV: Tooth and Claw)
Sir Doctor of TARDIS: After being knighted under this name, the Doctor tried to use it when he met William Shakespeare. Shakespeare's mind could not be swayed by psychic paper used to show his title. (TV: The Shakespeare Code)
Doctor Vile: The Doctor briefly masqueraded as the space pirate Doctor Vile to stop a war between humans and intelligent insects. (TV: The Infinite Quest)
Doctor McCoy: After a discussion with Donna Noble, in which she compared the sonic screwdriver to Star Trek's tricorder, the Doctor used the alias Dr McCoy (after Dr. Leonard "Bones" McCoy) when dealing with a group of soldiers (Donna called herself Captain Kirk, after James T. Kirk). (AUDIO: Pest Control)
Spartacus: When visiting Pompeii in 79 A.D, the Doctor and Donna both called themselves 'Spartacus', been a minor joke. (TV: The Fires of Pompeii)
Chief Inspector Smith from Scotland Yard: Used when involved with the death of Professor Peach. (TV: The Unicorn and the Wasp)
Doctor Noble: The Doctor used this when investigating the Ood Industries claiming Donna and he were from the Noble Corporation. (TV: Planet of the Ood)
Actors: When visiting Hollywood in the early 20th century, the Doctor adopted a number of Hollywood-related names whilst attending a party. Within the space of a few minutes, he called himself "Tom Cruise," "Michael Caine," "Pee-Wee Herman," and "Tom Hanks." (COMIC: Silver Scream)

Eleventh Doctor

Captain Troy Handsome of International Rescue: When introducing himself to a crashed time ship's avatar. (TV: The Lodger)
Commander Bond of Naval Intelligence: An alias used by the Doctor when he encountered Gein. (DWAN: Sub-species)
The Anti-Squid: A title the Doctor put little thought into due to the lack of preparation time. Meaning of the title is that he is the Devil of the space squid religion. (PROSE: Space squid)
Fred Astaire: An alias he used when asked to sign his name for a magic show audition. (PROSE: Magic of the Angels)
The Caretaker: Alias used when Madge, Lily and Cyril Arwell stayed with him in a dilapidated house in Dorset. (TV: The Doctor, the Widow and the Wardrobe) In the same episode, he follows this up by saying he is either called the Caretaker or "Get off this planet." "Though," as he points out, "strictly speaking that probably isn't a name."
Sherlock Holmes: used to gain entry to Dr Simeon's institute. Strax even called the Doctor this a few times just to annoy him. (TV: The Snowmen)
Pro Consol: Alias used during his adventure at Hedgewick's World of Wonders to keep a punishment platoon from being hostile to him and his guests. (TV: Nightmare in Silver)

Nicknames

A list of names other individuals have called the Doctor throughout his travels.