This is a list of alternate timelines, universes and other types of realities.

Canon base reference 
The most commonly encountered timeline is known as the "canon" universe or "primary" universe. The history of this reality includes the known history of Earth, the Federation, with events known until around the Terran year 2379. While generally continuous in and of itself, there are numerous time-travel scenarios and other reality-distorting events that have created discontinuities that, in some respects, could be considered parallel universes or timelines.
Mirror universes 
This is a group of realities where the Federation has evolved into a Terran Empire. Numerous alternate universes are known to branch from this reality.
The Doomsday War 
This alternate reality was caused by an alien weapon sent back in time to destroy the USS Enterprise. The weapon was successful and plunged the Alpha Quadrant into a terrible war. Dozens of worlds including Vulcan were destroyed as the machines began to multiply. (Star Trek: New Voyages: "In Harm's Way
Pendragon universe
This alternate reality diverged from the primary universe in early 2372 after Admiral James Leyton's coup on Earth was successful and triggered the start of a Federation Civil War. (Star Trek: Pendragon)
Alternate reality
While the term "alternate reality" is widely-used, the term also specifically refers to the alternate timeline created when Nero traveled back in time and destroyed the USS Kelvin. (Star Trek; Star Trek Into Darkness)
Remington universe
This alternate reality diverged from the primary universe at an unknown time before humanity's discovery of warp drive, yet the reality was similar to the prime universe in many ways. (Star Trek: Remington)