Genocide

Genocide was the destruction or attempted destruction of either an entire species or specific group of people. It can be contrasted with murder, which involved the killing of individuals rather than entire populations.

The Doctor seemed to be vehemently opposed to genocide, especially if there was an alternative to ending the conflict; his tenth incarnation claimed that, if one looked up the word "genocide" in a dictionary, they would see a picture of him with the caption "over my dead body", (TV: The Doctor's Daughter) while the eleventh insisted that genocide was never a solution, even in a seemingly endless war like that between the Sontarans and the Rutans. (GAME: The Gunpowder Plot) However, he himself resorted to it, intentionally or otherwise, on several occasions.

Human genocides
When Brigadier Lethbridge-Stewart destroyed the Wenley Moor Silurian colony, the Third Doctor was disgusted by the act, considering it genocide. (TV: Doctor Who and the Silurians)

Bennett believed that he had wiped out the Didonians. However, at least two had survived. (TV: The Rescue)

Humans may have committed near-genocide against the Wirrn in Andromeda when they destroyed their Breeding Colonies. (TV: The Ark in Space)

The Fourth Doctor helped human scientists kill the last of the Pescaton by the application of high-frequency sound waves. The Pescatons had fled their dying homeworld in search of another planet with large areas of salt water that could support them. (AUDIO: Doctor Who and the Pescatons)

Koel Paddox destroyed the entire Arboretan race as part of his efforts to duplicate their ability to live their lives over again while trying to change his past (PROSE: Festival of Death).

The Eleventh Doctor accused the pirate Solomon of genocide after finding out he ejected the Silurians on-board their Ark into space. (TV: Dinosaurs on a Spaceship)

Dalek genocides
As the Daleks believed in racial purity and their superiority, they were responsible for many acts of genocide during their history. Races they destroyed included: Koral's species (PROSE: Prisoner of the Daleks) and Eve's species. (TV: The Mad Woman in the Attic)

The Daleks wiped out the last Mechonoids on Magella (although considering that the Mechonoids were robots and not technically a living species, whether this counts as genocide is debatable). (PROSE: Birth of a Legend)

Dalek Caan committed genocide by killing all the Dalek-humans when they refused to obey the Daleks. When the Doctor confronted him, he offered help as he had already seen one genocide and had no wish to cause another. (TV: Evolution of the Daleks)

Daleks of the New Dalek Empire destroyed the Tactires reducing to one individual. (COMIC: The Forgotten)

The Markhan Genocide was considered one of the Daleks' greatest atrocities. (PROSE: The Ripple Effect)

Doctor genocides
The Fourth Doctor destroyed Sutekh, the last known Osirian. He even taunted Sutekh as he died in the "temporal trap", asking him how long Osirians live, before finally declaring, "The time of the Osirans is long past. Go." (TV: Pyramids of Mars) The Fifth Doctor encountered further Osirians, (PROSE: The Sands of Time, AUDIO: The Bride of Peladon) but was forced to destroy them as well.

The Fourth Doctor killed Eldrad, the last Kastrian. (TV: The Hand of Fear) He later encountered another surviving Kastrian, Mulkris, assigned to ensure that Eldrad's sentence was carried out. (AUDIO: Eldrad Must Die!)

With Leela's help, the Fourth Doctor destroyed the last of the Fendahl. He dropped the remains of the Fendahl into a supernova to ensure their permanent destruction. (TV: Image of the Fendahl) However, this attempt appeared to have failed, as the Fendahl later managed to re-manifest in Kaldor City, (AUDIO: Checkmate) and it was later revealed that the Fendahl defeated here was only a fragment of the true Fendahl that remained trapped on Planet 5 (although the true Fendahl was consumed by the Fendahl Predator). (PROSE: The Taking of Planet 5)

The Fourth Doctor fulfilled a Time Lord's solemn duty by killing the King Vampire, the last of the Great Vampires and sole vampire survivor of the Vampire-Time Lord war. (TV: State of Decay)

When the Sixth Doctor was forced to wipe out the Vervoids to stop them killing the humans on Hyperion III, this was used against him in a trial occurring in his own past. When the Valeyard accused the Doctor of genocide, the Doctor said that he had no other option. (TV: Terror of the Vervoids) When the Eighth Doctor travelled to the events of the trial and met his sixth incarnation, he dismissed the charge due to the artificial nature of the Vervoids' creation. (PROSE: The Eight Doctors)

The War Doctor committed double genocide when he destroyed the Time Lords and most of the Daleks at the end of the Last Great Time War in an alternate timeline. It was apparently Rassilon's Ultimate Sanction, which threatened the whole universe, that convinced him he had no other choice. (TV: The End of Time) With the help of the Tenth and Eleventh Doctors, he found a different solution and with the help of "all thirteen" incarnations of himself, froze Gallifrey and the Time Lords in a pocket universe while the Daleks destroyed themselves. (TV: The Day of the Doctor)

During the Dark Times, the Fledgling Empires all but wiped out the Racnoss to prevent their devouring of planets. The Tenth Doctor later made them extinct when he flooded a ship of surviving young within the Earth. He was unknowingly aided by, who ordered the destruction of the Webstar which resulted in the death of the Empress of the Racnoss. (TV: The Runaway Bride)

The Doctor accused his Meta-Crisis duplicate of genocide when he destroyed all the Daleks in the Medusa Cascade, along with their fleet and the Crucible. (TV: Journey's End) It was later revealed that at least one Dalek Saucer, with three surviving Daleks on board, managed to escape, and they were able to rebuild their race using Progenitors. (TV: Victory of the Daleks)

The Saturnyns were wiped out, with the Eleventh Doctor's help, in their attempt to take over Earth and convert female humans into new mates for their males. The converts were killed in an explosion, leaving the males to die out. The last female, Rosanna Calvierri, offered herself as a last meal to them, after telling the Doctor she hoped that their extinction would haunt his conscience. (TV: The Vampires of Venice)

Other genocides
By the time of the Thousand Year War between the Kaleds and the Thals on Skaro, the Kaleds had wiped out the Dals and the Tharons, the two other sentient humanoid races who had evolved on the planet. (AUDIO: Purity)

The Caxtarid wiped out four indigenous sentient species on Kapteyn 5 after their conquest of the planet. (PROSE: The Room With No Doors)

After the death of all his species, Androvax went on a vengeful vendetta, destroying twelve planets before finally being arrested by the Judoon when he attempted to destroy Earth. (TV: Prisoner of the Judoon)

When the Weeping Angels arrived on Alfava Metraxis, they wiped out the Aplans. (TV: The Time of Angels)

The Eleventh Doctor considered the complete destruction of the Cybermen at the hands of the Borg in the Federation universe genocide, although Captain Jean-Luc Picard did not share his grief. (COMIC: Assimilation²)

Planned genocides
The Voord on Kandalinga planned to wipe out the native Fishmen once they were no longer of use to them, but were stopped by the First Doctor. (PROSE: The Fishmen of Kandalinga)

Qar, the leader of an unnamed planet, planned to massacre the Tryods so that her people could exploit the mineral wealth of the lands on which the Tryods lived. The massacre was prevented by Asiries, who was convinced to do so by the Second Doctor. (PROSE: The Word of Asiries)

The Bannermen attempted to bring about the extinction of the Chimerons. Only Delta escaped, along with an egg, and after Billy converted into a Chimeron, the species could continue. (TV: Delta and the Bannermen)

Miss Myers, a member of a fleshkind race, created a child, intending for her to exterminate the metalkind. This plot was foiled by Sarah Jane Smith. (TV: Sky)

Rivesh Mantilax invented a genetic weapon that would allow him to destroy the entire Viperox race. The Tenth Doctor stopped him from using it, insisting that no one had the right to wipe out a whole species. However, he did modify the device to merely impede the Viperox, halting an attempted invasion of Earth and driving Lord Azlok and the aggressors back to Viperon. (TV: Dreamland)

The Shakri desired to destroy the human race, whom they considered "pests", but were stopped by the Eleventh Doctor. (TV: The Power of Three)

Rassilon attempted to deploy the Tear of Isha into Tantalus Eye, killing all life. But that plan was stopped by the War Doctor (PROSE: Engines of War)

Behind the scenes

 * According to the Decide Your Destiny book, The Corinthian Project, the Dax were almost wiped out by the Daleks. However, because the novel has multiple possible endings, it's difficult to assert with certainty that the event ever occurred.