TARDIS telephone
A telephone capable of calling and receiving calls from anywhere in time and space was present in the TARDIS console rooms of the Eighth, (AUDIO: Their Finest Hour) Ninth, (TV: World War Three) Eleventh (TV: The Beast Below, The Snowmen) and Twelfth Doctors, (TV: Before the Flood) as well as within the police box plasmic shell of the Doctor's TARDIS. (TV: The Bells of Saint John, The Day of the Doctor, Time Heist)
The number of Martha Jones' mobile phone, at the time the Tenth Doctor kept it aboard the TARDIS after she gave it to him, was 07700 900461. (TV: The Stolen Earth) This number later became the number for the phone inside the police box shell. (TV: The Day of the Doctor) Later, the TARDIS telephone number was changed to 95475949, (COMIC: The Swords of Kali) and later still to 0800 678 3110. (PROSE: Have You Seen The Aliens Terms and Conditions [+]Loading...["Have You Seen The Aliens Terms and Conditions (feature)"] et al.)
As early as the Doctor's eighth incarnation, the TARDIS had within it a telephone, somewhere other than the console, but very few people knew about it. Its existence was kept a secret, shared only with the "very finest" of history. Among those who did have the number were Ringo Starr, Winston Churchill (AUDIO: Their Finest Hour) and Tiger Maratha. (COMIC: The Swords of Kali) Later incarnations made greater use of the telephone, but the Twelfth Doctor wanted to keep his phone number a guarded secret, so that not just "anyone" would be able to contact him. (TV: Face the Raven)
The Eleventh Doctor twice used the TARDIS telephone to contact others earlier or later on in his own time stream. (TV: The Day of the Doctor, Deep Breath) The Eleventh Doctor joked that if someone were to call the TARDIS from another era, their phone bill would be quite costly. (TV: The Bells of Saint John)
A dummy phone
The police box phone rang when the Seventh Doctor got the Perivale police to call the ID number on his UNIT pass, thus allowing him and Ace to enter the TARDIS. (PROSE: Cat's Cradle: Time's Crucible) When Jamie used Om-Com to call the police box phone, the Ninth Doctor said it wasn't possible — that phone was just a dummy. (TV: The Empty Child) The external phone was impossibly called again in the Doctor's eleventh incarnation, by Clara Oswald, having been given the number (TV: The Bells of Saint John) by Missy. (TV: Death in Heaven) Clara continued to call this phone into the Doctor's twelfth incarnation. (TV: The Time of the Doctor, Time Heist)
On the console
During his travels with Liv Chenka and Helen Sinclair, the Eighth Doctor had a telephone built into the TARDIS console.
While stranded in London, 2020, he had the TARDIS telephone number listed on his mobile phone as "The Missus", to Liv's surprise and delight. Liv and Helen tried calling the Doctor after he ran off in the TARDIS to try to save Andy Davidson, but only reached the answerphone until the Doctor's final moments in this timeline. (AUDIO: Get Andy)
The Ninth Doctor's TARDIS console also had a phone. Rose Tyler was surprised to find it had one when the Doctor called her with it. "You think I can travel through space and time and I haven't got a phone?" It showed up on her call display as "Tardis". (TV: World War Three)
Nevertheless, the Tenth Doctor never used it, and instead made use of the mobile Martha Jones gave him for all incoming and outgoing calls. (TV: The Sontaran Stratagem/The Poison Sky, The Stolen Earth)
Jackie Tyler had the Doctor's TARDIS phone number, while the Ninth Doctor had never given it to Jack Harkness. (AUDIO: Wednesdays For Beginners)
Following that console room's destruction and the TARDIS's "regeneration" into a new one, (TV: The Eleventh Hour) though, the Eleventh Doctor's TARDIS had one on the control console. Amy Pond was surprised to find a telephone in the Doctor's ship when Winston Churchill called; the Doctor replied, "It's a phone box." (TV: The Beast Below) In a psychic pollen-induced shared dream, Rory Williams suggested calling for help using the TARDIS phone as they approached a cold star. (TV: Amy's Choice)
Just after Rory and Amy's wedding, the Eleventh Doctor was informed by phone about an Egyptian goddess loose on the Orient Express, in space. (TV: The Big Bang) It was also through this telephone that the Doctor was informed of the Brigadier's death. (TV: The Wedding of River Song) This console phone had a cord long enough that its user could use it outside. (TV: Day of the Moon, WC: Pond Life) It also had an answering machine. (WC: Let's Kill Hitler Prequel, The Doctor, the Widow and the Wardrobe Prequel)
The Eleventh Doctor's next TARDIS also had a phone, and Vastra called it to tell him Clara Oswald satisfied the "one-word test" with the "pond". (TV: The Snowmen) The interior phone was rarely used, though, as, after Clara impossibly called him on the exterior police box phone, (TV: The Bells of Saint John) calls were directed to that phone instead. (TV: The Time of the Doctor, Time Heist)
Exterior telephone
During the latter part of the Eleventh Doctor's life, and early Twelfth Doctor's, all incoming and outgoing calls were made through the telephone on the TARDIS's outer plasmic shell. (TV: The Time of the Doctor, Time Heist) To call Kate Stewart, he was forced to hang outside of the TARDIS to reach it, as the TARDIS was in the air being transported by helicopter. (TV: The Day of the Doctor) Similarly, when Clara called him while he was orbiting Trenzalore with enemy ships surrounding him, he had to quickly reach out to get the phone. He gave Handles the command to remind him to patch the telephone back through the console unit to finally fix the problem, and this reminder ended up being Handles' final words before malfunctioning and "dying". (TV: The Time of the Doctor)
After destroying the Daleks and ending the Siege of Trenzalore, the Eleventh Doctor retreated to the TARDIS before completing his regeneration and used the TARDIS phone to contact Clara from his future already travelling with his next incarnation to reassure her that he was still the Doctor despite having changed his appearance. He neglected to hang the phone back up afterwards. The Clara from his present came across the TARDIS and hung it up for him. She remembered doing this when she received the Eleventh Doctor's call while in the company of the Twelfth Doctor, allowing her to piece together the puzzle and accept that what the Doctor was telling her was true. (TV: The Time of the Doctor, Deep Breath)
Despite Handles' reminder to fix it, the Twelfth Doctor initially continued to use the exterior phone. He gave Karabraxos his phone number, which she used to call him in the past and set him and Clara on their heist in the Bank of Karabraxos. (TV: Time Heist) Clara also called this phone when she contacted the Doctor after the death of Danny Pink. (TV: Dark Water) When the Eleventh Doctor phoned Clara prior to his regeneration she was unable to tell who was calling until she answered. (TV: Deep Breath)
Tiger Maratha called this phone when the Twelfth Doctor and Clara were visiting Leonardo da Vinci in Florence. Maratha was given the phone number by the Fourth Doctor. (COMIC: The Swords of Kali)
Patched through the console unit
The Twelfth Doctor eventually did reconnect the interior phone, and used it to contact Clara for a private part of a phone conversation between the two. (TV: Before the Flood) Calls were once again directed to it, as Rigsy was able to use the Doctor's phone number to call the console phone. The Doctor was unhappy that his phone number was being shared about; Clara had given the number to Rigsy for emergencies. (TV: Face the Raven)
Mechanics
Phoning the TARDIS would send the user's call through the Time Vortex. The TARDIS, having the ability to see all of time and space at once, would direct the call to the intended point in the Doctor's time stream. However, the call could sometimes fail to connect. In that case, the TARDIS would re-route the phone call to the best possible alternative. (TV: The Pandorica Opens) Outgoing calls from the TARDIS functioned in the same way.