Alternate timeline

An alternate timeline was a reality that diverged from the "true" timeline due to the actions of time travellers or other temporal phenomena. They were different from parallel universes in that they did not separate cleanly at the point of creation resulting in the new timeline destroying the old one. (PROSE: Imperial Moon)

Physics

Alternate timelines could be visited accidentally by contact with a time track (TV: The Space Museum, AUDIO: The Mutant Phase) or other anomalies (AUDIO: Colditz) in the Time Vortex. Deliberate travel to these timelines was possible if the traveller possessed something, such as the sigil ring, that allowed them to change time streams. (PROSE: Goth Opera)

They may have diverged from points in history where there was temporal fluctuation, but beings with enough power were capable of changing time enough to create them, such as Sutekh and the Chronovores. Because the universe only had a finite amount of mass and energy, the creation of an alternate timeline adversely affected the real timeline, causing chaos throughout the universe; releasing enough energy could destroy the timeline and set history back on its correct course. (PROSE: Blood Heat)

Though a timeline may be negated, memories of it could still be retained. (TV: The Big Bang, The Impossible Astronaut)

Timelines encountered by the Doctor

Timeline	Negated By	Featured in
The First Doctor and his companions become exhibits in the Moroks' Space Museum	First Doctor, Ian Chesterton, Barbara Wright, Vicki	TV: The Space Museum
Barbara Wright marries Ptolemy I and becomes Queen of Alexandria	Alternate Barbara	PROSE: The Book of Shadows
WOTAN conquers Earth (this was the correct timeline before it was changed by the Doctor)	First Doctor	PROSE: The Time Travellers, TV: The War Machines
Nancy Grover uses Grold technology to become a goddess	Third Doctor and Liz Shaw	PROSE: The Eye of the Giant
The Power Elite take over Earth	Third Doctor	PROSE: Prisoners of the Sun
Freedom fighters from the 22nd century assassinate Sir Reginald Styles	Third Doctor and Jo Grant	TV: Day of the Daleks
Theodore Cassells's experiments lead to a global war which devastates Earth	Third Doctor	COMIC: A Stitch in Time
The Third Doctor dies on Dust and regenerates	Eighth Doctor by destroying Gallifrey (PROSE: The Ancestor Cell)	PROSE: Interference - Book One, Interference - Book Two
Sutekh is freed and devastates Earth	Fourth Doctor and Sarah Jane Smith	TV: Pyramids of Mars
Daleks undergo the Mutant Phase	Dalek Emperor	AUDIO: The Mutant Phase
Melanicus creates the Millennium Wars	Fifth Doctor, Sir Justin and Shayde	COMIC: The Tides of Time
Humans evolve into Haemovores	Seventh Doctor and Ace	TV: The Curse of Fenric
The Dark Matrix terrorises England	Seventh Doctor and Ace	PROSE: Matrix
The Nazis win World War II after a piece of laser technology is left at Colditz Castle	Alternate Eighth Doctor and Elizabeth Klein (inadvertantly)	AUDIO: Colditz, Klein's Story
Vladimir Khrushgov succeeds Konstantin Chernenko as leader of the Soviet Union causing World War III to occur in 1989	Seventh Doctor	AUDIO: Protect and Survive
Adolf Hitler uses the Timewyrm's power to enable Nazi Germany to conquer Earth	Seventh Doctor and Ace	PROSE: Timewyrm: Exodus
Chad Boyle kills Dorothy McShane with a brick to the head	Ace	PROSE: Timewyrm: Revelation
The Process enslaves the Time Scaphe crew	Seventh Doctor	PROSE: Cat's Cradle: Time's Crucible
Silurian Earth	Destroyed, not negated, by Seventh Doctor	PROSE: Blood Heat
Alternate timeline (Time & Time Again)	Seventh Doctor, Ace and Bernice Summerfield	COMIC: Time & Time Again
The Knights of Velyshaa conquer Gallifrey	Fifth Doctor, Sixth Doctor, Seventh Doctor, the Temperon	AUDIO: The Sirens of Time
Humans don't evolve and Earth is a Tractis colony known as Paratractis	Eighth Doctor, Sam Jones, Jo Grant	PROSE: Genocide
Sato Katsura forms the Church of the Glorious Dead; the Church, led by Sato, conquer Earth and rename it Dhakan; the Church begin invading and massacring other planets they view as "unbelieving"	Kroton	COMIC: The Glorious Dead
Pete Tyler doesn't die and Reapers begin consuming humanity	Pete Tyler	TV: Father's Day
The Year That Never Was	Tenth Doctor, Martha Jones and Captain Jack Harkness	TV: Last of the Time Lords
Donna's World	alternate Donna Noble, with assistance from Rose Tyler	TV: Turn Left
The Progenitor Daleks repopulate Skaro and exterminate humanity to extinction in 1963	Eleventh Doctor and Amy Pond	GAME: City of the Daleks
The Doctor's TARDIS explodes, creating Cracks in Time which begin erasing the universe's history	Eleventh Doctor, Amy Pond, Rory Williams (Auton) and River Song (TV: The Big Bang)	TV: Series 5
Amy Pond is stranded on Apalapucia for 36 years	Eleventh Doctor	TV: The Girl Who Waited
River Song's World	Eleventh Doctor, Amy Pond, Rory Williams, River Song, the Teselecta	TV: The Wedding of River Song
The Silurians attempt pump poison onto Earth's surface to reclaim it	Eleventh Doctor and River Song	GAME: The Eternity Clock
The Progenitor Daleks invade and destroy London in or before 2106	Eleventh Doctor and River Song	GAME: The Eternity Clock
The Cybermen conquer the galaxy	Eleventh Doctor and Jean-Luc Picard	COMIC: Assimilation²
Rory Williams remains imprisoned in Winter Quay for the rest of his life	Rory Williams, Amy Pond	TV: The Angels Take Manhattan

Timelines encountered by others

Timeline	Negated By	Featured in
Andrea Yates' World	alternate Andrea Yates	TV: Whatever Happened to Sarah Jane?
The Trickster's World	Eddie and Barbara Smith	TV: The Temptation of Sarah Jane Smith
Ship erases Sarah Jane Smith, Luke Smith and Clyde Langer	Adam Lloyd	TV: The Mad Woman in the Attic