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) The Tenth Doctor admitted that, for the Daleks, their history was "confusing enough" before they entered into the Time War. (PROSE: Prisoner of the Daleks)

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. The Doctor himself was traveling with Sheena when he become embroiled in the Time War as its effects changed Sheena to Emma then Louise before erasing her from existence entirely, with even the Doctor forgetting his former companion. The Theseus, the spaceship they had visited, changed from a luxury liner to a ship carrying refugees fleeing the conflict. (AUDIO: The Starship of Theseus) Following exposure to a significant number of alternate timelines shown in Professor Deepa's quantum visualiser, the Doctor regained his memories of both Sheena and Emma. (AUDIO: State of Bliss)

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)

The Aubertides pursued the Seventh Doctor to England prior to the First World War, where he was disguised as a human teacher named John Smith. (PROSE: Human Nature) A similar incident occurred when the Tenth Doctor became John Smith in an attempt to elude the Family of Blood. (TV: Human Nature/The Family of Blood) Daughter of Mine, of the Family of Blood, was aware that this was a "story that happened many times in many ways", not all of which she was present for. (AUDIO: Shadow of a Doubt)

The Seventh Corsair claimed to her parrot that the destruction of Skaro by the Hand of Omega triggered a smaller-scale time war preceeding the Time War. According to her, this smaller, premature conflict was eventually erased by the larger one along with all memory of it ever happening. (PROSE: One Virtue, and a Thousand Crimes)

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 Unon of Zentauron were originally peaceful explorers before they were decimated by the Time War. In its aftermath they used weapons salvaged from the conflict to forge themselves as warriors and were among several factions which sought to seize the vacuum left behind by the Time Lords, in addition to the Cybermen and the Sontarans. The newly established New Dalek Paradigm was content to leave such "upstarts" to the Doctor. (COMIC: Weapons of Past Destruction, PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

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)

Other influences
When they saw the Daleks emerge from the shadows on a war footing, (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) the Time Lords had sent an activation signal to any N-Forms laying dormant throughout history. (AUDIO: Desperate Measures) The Seventh Doctor, Chris Cwej, and Roz Forrester encountered one reactivated N-Form in 1987 Britain and stopped it from destroying the Earth. During a confrontation, the N-Form told the Doctor that its reactivation signal came from the future, taunting him by asking if Gallifrey had forgot to warn him that "the War's started all over again." (PROSE: Damaged Goods, AUDIO: Damaged Goods) The Doctor later confirmed that a deliberate reactivation impulse had been sent from the future to dormant N-Forms throughout time, with another N-Form being responsible for the destruction of the Quoth homeworld. He faintly traced parts of the signal to the 30th century, (PROSE: Damaged Goods) where he discovered that the Brotherhood of the Immanent Flesh had some responsibility for the N-Forms. (PROSE: So Vile a Sin)

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 to the Second Dalek War, (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)

In addition, the Doctor encountered both his fourth incarnation and a force of Daleks from the Second Dalek War at the Cathedral of Contemplation, which existed outside of spacetime. (AUDIO: Out of Time) Indeed, incarnations of the Doctor preceding, living through and postdating the Time War came into contact on many occasions. (TV: Time Crash, The Day of the Doctor, Fugitive of the Judoon, WC: Doctors Assemble!) On one of these Multi-Doctor Events, the First Doctor was made aware by the Testimony Foundation that he would become known as the "Doctor of War", a prospect which initially disturbed him before he realised its meaning as demonstrated by the Twelfth Doctor, "a couple fewer dead people on the battlefield". (TV: Twice Upon a Time)

During the Kotturuh crisis, the Tenth Doctor was surprised to encounter a version of the Dalek Empire which had no recollection of fighting the Time War. (COMIC: Defender of the Daleks)

Clara Oswald, a companion of the Eleventh Doctor, entered the Doctor's time stream to save him from the Great Intelligence, entailing the creation of numerous splinters of Clara whom were present across the Doctors lives, including a direct encounter with the First Doctor as he escaped from Gallifrey. (TV: The Name of the Doctor)

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

After acquiring a fragment of the Eternity Clock, the New Dalek Paradigm, led by a new Emperor, tested its power by locking 2106 London in a time bubble. Their plan was to expand the temporal field to swallow the entire planet Earth, thus cutting it off from history. Once perfected, the Eternity Clock trap would allow the Daleks to freeze any planet that had ever existed, with the Emperor anticipating the total "obliteration" of Gallifrey. However, this plan was thwarted by the Eleventh Doctor and River Song, who deactivated the time lock and recovered the Eternity Clock. (GAME: The Eternity Clock)

The discovery of a wrecked New Paradigm Supreme Dalek in a Renegade Dalek base on Thule suggested to historians some interference from the future Dalek faction in the Imperial-Renegade Dalek Civil War. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

By one account, the Time Lords restored the pre-Time War timeline following their return to the universe, undoing the various temporal changes inflicted by the war. Among those impacted by this were the Voord, with the evolution they had undergone during the war being reversed despite their efforts to prevent such an outcome in an alternate timeline. (COMIC: Four Doctors)

Behind the scenes
John Dorney has addressed the Time War's effect on the timeline. "But in terms of the Doctor's timeline (and that of the Time Lords and Daleks) there clearly is a universe in which they're not fighting the Time War (the classic series), and a universe when the Time War is over and done (the new series) and the Doctor has crossed from one to the other (despite this basically being borderline impossible). So the Doctor can literally be in the exact same time and place but on different sides of the war. If that's a little confusing, I'd argue that's exactly how it should be as the Time War is a battle fought by beings who live four dimensionally and shouldn't be wholly comprehensible to those of us who have to limit ourselves to three."

- John Dorney