Pre-Time War universe

As noted by historians studying the Daleks, the version of the Doctor's universe that had "first felt the winds of change" preceeding the Last Great Time War was not the same as the universe that eventually survived the conflict. The Time War itself was time locked to its own timeline following the fall of Gallifrey. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

Discrepencies with the post-Time War universe
In the universe before the Time War, the Time Lords' existence enabled travel to parallel universes, (TV: Rise of the Cybermen) and they would have acted to prevent Reaper incursions at wounds in time. (TV: Father's Day) In their absence in the post-Time War universe, paradox eaters such as Reapers, Chronovores and Gramoryans ran wild, (AUDIO: Divorced, Beheaded, Regenerated) and travel to parallel universes became nearly impossible. (TV: Rise of the Cybermen)

One known discrepency between the pre and post-Time War universes was the life of Bliss. In the pre-Time War universe she studied robotics and never encountered the Doctor, (AUDIO: Companion Piece) whereas in the post-Time War universe she studied quantum physics and travelled with the Eighth Doctor. (AUDIO: The Starship of Theseus)

In the original versions of the Third Doctor's encounters with the Daleks at Auderly House and in the 26th century Ogrons were not present. Their roles in the conflicts were retrospectively added during the Time War by the Dalek Overseer as an experiment, though he found their addition made no difference to the events' outcomes. (AUDIO: Planet of the Ogrons)

In the original timeline, the First Doctor travelled to the South Pole immediately after his adventure in 17th century Cornwall. (AUDIO: The Plague of Dreams) The course of his life was later diverted by interference caused by the Time War era Daleks, (AUDIO: The First Doctor: Volume Two trailer) requiring the Time Lords to send the Player to put events back on course by directing the Doctor to the South Pole. (AUDIO: The Plague of Dreams)

Originally the planet Gernica existed until at least the 64th century, when it was visited by the Sixth Doctor and Evelyn Smythe. During the Time War however the planet was destroyed on the 14th August 3097. (AUDIO: Death Will Not Part Us)

Entire species were eradicated by the Time War, and the Gelth needed to take on a gaseous form to survive. Some of the races that fell, including the Malfinions, Hederons, Scarbians, were so completely removed from time that, after the war ended, their names only survived as footnotes in old Time Lord records, later being mentioned in a historical chronicle as well. In fact, no one in the universe even remembered these races existed. (PROSE: The Whoniverse) Several races which were erased from existence during the war persisted as echoes displaced from time on a plane of non-reality, banding together to become the Bygone Horde. The Ninth Doctor thwarted their plan to return to existence, as it would have entailed the sacrifice of the human race. (AUDIO: The Other Side) As related by the Doctor to Rose Tyler, the Nestene Consciousness was originally a flesh and blood organism with an affinity for plastic before the war "rewrote its DNA" so that it became a living plastic lifeform itself. (PROSE: Rose)

The Tenth Doctor claimed that before the Time War the universe was full of "pseudo-gods and quasi-deities" which were not present after the conflict. (AUDIO: The Lost)

Access after the Time War
It was possible for time travellers in the post-Time War universe to arrive in the pre-Time War universe. Twice the Tenth Doctor found himself in the pre-Time War universe, firstly when his TARDIS accidentally jumped a time track, (PROSE: Prisoner of the Daleks) and secondly due to being paradoxically abducted by his own future self using George Sheldrake's time tunnels. (AUDIO: Buying Time) The Doctor was able to use a Dalek time machine to fly through the temporal event horizon to return to the post-Time War universe. (AUDIO: The Triumph of Davros)

River Song also once found herself in the pre-Time War universe. (AUDIO: Companion Piece)