Positive-time universe
By some accounts, the Doctor lived in the universe of positive-time, also known as Rassilon's continuity, a reality created and maintained by a positive Web of Time which separated it from anti-time and the wider antiverse. (AUDIO: Neverland, Zagreus)
One account suggested that this universe was not synonymous with the Doctor's universe as a whole; this particular Web of Time only allowed one possible history, and the outside anti-time was connected to billions of alternative realities, some of which had other Doctors who were just as primary as the positive-time Doctor. (AUDIO: Zagreus) Other accounts, however, showed it to indeed be synonymous with the Doctor's universe as a whole. (AUDIO: Mary's Story, The Zygon Who Fell to Earth, COMIC: Vortex Butterflies)
The period during which this universe was defined by its positive-time nature was connected to several interlinked sequences in the lives of the Fifth, Sixth, Seventh, and Eighth Doctors, (AUDIO: The Apocalypse Element, The Time of the Daleks, Neverland, Zagreus, et al.) as well as some factions in their vicinities. (AUDIO: Invasion of the Daleks, Weapon of Choice, et al.) These sequences were further deeply intertwined with others across the Doctor's lives (AUDIO: 100, Prisoners of Fate, Companion Piece, et al.) and the wider universe. (AUDIO: The Screaming Skull, The Split Infinitive, et al.)
Fate
By one account, this reality, while separate during the Doctor's time with Charley Pollard, later merged with other prominent parallel timelines of the Doctor's life during the Last Great Time War. (PROSE: The Eighth Doctor Part 2) The Eighth Doctor acknowledged Charley as well as Fitz Kreiner, C'rizz, Lucie Miller, Tamsin Drew and Molly O'Sullivan before his regeneration into the War Doctor. (PROSE: The Day of the Doctor, TV: The Day of the Doctor)
Relation to other realities
The positive-time universe ran parallel to a universe with a different version of the Doctor's life which included the Eighth Doctor travelling with Destrii. (PROSE: The Eighth Doctor Part 2) When Ace was shown her future, she saw "several universes" of possibilities, including one where she was surrounded by giant fleas. (AUDIO: Signs and Wonders) Exposed to anti-time, the Eighth Doctor saw a version of himself from this universe on Oblivion fighting the Horde. (AUDIO: Zagreus)
The positive-time universe was distinct from another version of the Seventh Doctor's life in which Romana's Presidency went slightly differently. (AUDIO: Zagreus) Among the several universes in Ace's possible futures was one where she rode on a moped in Paris. (AUDIO: Signs and Wonders) By the time the Eighth Doctor travelled with Charley, Grant Markham had been erased from history. (PROSE: Repercussions...)
Another anti-time universe was one where the Eighth Doctor's heart was removed. (AUDIO: Zagreus) This universe's Sixth Doctor had a different version of his travels with Evelyn Smythe (PROSE: Instruments of Darkness) and later witnessed the positive-time Doctor and Evelyn during a multiversal adventure. (PROSE: Spiral Scratch) By the time the Eighth Doctor travelled with Charley, Sam Jones had been erased from history. (PROSE: Repercussions...)
From the centre of the Time Vortex, the Valeyard of a parallel universe observed the timeline where the Doctor's companions included Evelyn Smythe, Hex, Charlotte Pollard, and C'rizz. (AUDIO: He Jests at Scars...)
By one account, whilst travelling with the Seventh Doctor, Ace was shown multiple possible futures in her timeline by a Quantum Anvil, which included her coming to live on Gallifrey. This incident led her to leave the Doctor. (PROSE: At Childhood's End)
The positive-time universe was connected to Lethbridge-Stewart's universe via Sunyata, which spanned all realities. (PROSE: Night of the Intelligence) When Counter-Measures fought the Great Intelligence in 1974, (AUDIO: Time of the Intelligence) Owain Vine witnessed it across realities via Sunyata, noting that he preferred that history to his own. (PROSE: Night of the Intelligence) Additionally, the Great Old Ones encountered by the Fifth Doctor, Erimem, and Peri Brown (AUDIO: The Roof of the World) were a parallel Sunyata-impression to the Great Intelligence of Owain's universe. (PROSE: Legacies)
In the reality of the Time War, the Time Lords recorded accounts of a Dalek presence on Strellin, the Dalek Time Controller and the Dalek Time Strategist, the latter of whom was said to be the mastermind behind Dalek victories in the conflict, as potentially apocryphal "anomalies". (PROSE: Dalek Combat Training Manual)
In the post-Time War universe, human historians were aware of unverified claims (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) that Davros, having survived the Duplicate Incident, came to be employed by Arnold Baynes, CEO of TransAllied, Inc, (AUDIO: Davros) and of stories of the 2180s Dalek invasion of Earth. (AUDIO: To the Death)
Behind the scenes
Gary Russell refers to this reality as the "Big Finish universe" in The Audio Scripts: Volume Four.