Alternate timeline

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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
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
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 Eleventh Doctor and Amy Pond GAME: City of the Daleks
The Doctor's TARDIS explodes, creating a Time Field which erases parts of history Eleventh Doctor, Amy Pond, Rory Williams (Auton) and River Song (TV: The Big Bang) TV: Series 5 (Doctor Who)
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 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