Retro-genocide

It was believed that before the War broke out, the interventionist elite of the Homeworld committed multiple retro-genocides on members of the lesser species, erasing them from history altogether, in secret. (PROSE: The Book of the War)

History
The Charons, a species with the ability to warp the fabric of the universe, were erased before they existed in the Time Wars by the Time Lords as they feared that no other life in the universe could co-exist with them. (PROSE: Sky Pirates!)

According to old lore, "fallen worlds" were taken over and turned into huge torture chambers by the Yssgaroth during their war with the Great Houses. As no traces of such atrocities remained in the subsequent version of history, it was commonly speculated that these worlds' existence was "retro-annulled" as an act of mercy by the Houses when they won the War, for all that such actions would later be made illegal in their culture. (PROSE: The Book of the War) Some accounts claimed instead that the depiction of the Great Vampires as wanton monsters was mere propaganda and the Vampires actually had a much more sympathetic agenda than arbitrary sadism, suggesting no such worlds may have ever existed in the first place. (AUDIO: Zagreus)

The Time Lords ordered the Fourth Doctor to erase or alter the creation of the Daleks during the Genesis Incident. (TV: Genesis of the Daleks, PROSE: Dalek Combat Training Manual)

The Last Great Time War between the Time Lords and the Daleks erased numerous species including the Malfinions, Hederons, Scarbians, who 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)

During the Time War, the Valeyard turned a temporal superweapon intended for use against the Time Lords against the Daleks, erasing the entirety of their race from the universe, save the Dalek Time Strategist who managed to escape into the multiverse. (AUDIO: The War Valeyard) With the Daleks erased, the Time Lords were unable to exactly recall who they had been fighting, leaving them to ponder who their mysterious, unknowable enemy had been. Not even the countless slaves the Daleks had the conscripted to serve as disposable troops could remember whom they had been serving under and so surrendered. (AUDIO: Dreadshade) By manipulating a parallel universe version of Davros, the Time Strategist used dimensional engineering to restore the Dalek Empire to existence, resuming the Time War. (AUDIO: Palindrome, Restoration of the Daleks)

The Daleks planned to erase the Voord of Marinus, who were allied with the Time Lords, but were foiled by the War Doctor. (COMIC: Four Doctors)

Alternate timelines
Witnessing a projection of what Gallifrey would be like under anti-time, the Eighth Doctor watched as a twisted version of Romana II, under the title of Imperiatrix, rejected the Dalek Emperor's plea for help. Despite the Emperor claiming that the Time Lords' "continuity" could not survive without the Daleks, the projection ended with Romana declaring its species enemies of the Time Lords and having the Emperor's entire fleet destroyed, wiping out the Daleks. This projection held that the Web of Time would fall into shreds and Gallifrey fell into corruption. (AUDIO: Neverland)

In an alternate timeline where the Cybermen allied with to invade the universe across its history, the Fifth Doctor discovered that the Cybermen had inhabited Skaro, having erased the Daleks from history. This timeline was negated when the Twelfth Doctor and Rassilon, who had been betrayed by the Cybermen, regenerated the universe. (COMIC: Supremacy of the Cybermen)