Evil

Evil was the concept or force perceived as being the opposite of what was good, both of them being part of moral duality. However, like good, evil could be perceived differently with conflicting views; as such, the Seventh Doctor claimed evil had no name. (TV: The Curse of Fenric)

In the distant past, the Grey Man's people imposed duality onto the first humanoids to evolve, resulting in them destroying themselves in chemical warfare. The Grey Man later created Cathedral as a metacultural engine that introduced "greyness" and "doubt" into the universe. (PROSE: Falls the Shadow)

The Time Lords did not believe in nor gave much thought to the concepts of good and evil, although the Doctor had always maintained that evil was a real force. (PROSE: Strange England, AUDIO: The Guardians of Prophecy) In his travels he met many "embodiments" of evil, including the Black Guardian, (TV: The Armageddon Factor) the Mara, (TV: Snakedance) Malador, (AUDIO: The Guardians of Prophecy), the Beast (TV: The Impossible Planet) and Fenric, whom the Doctor told Ace was one of two forces, only good and evil, that existed before the beginning of all time and space. (TV: The Curse of Fenric)

While the Doctor often tried to be a force for good, his methods could be seen as evil, causing other races to raise arms in fear against him, (TV: A Good Man Goes to War) with an alliance including several of his enemies imprisoning him in an attempt to prevent the end of the universe. (TV: The Pandorica Opens) Several individuals considered the Doctor's good to be their evil, including Sutekh (TV: Pyramids of Mars) and the Black Guardian. (TV: Mawdryn Undead)

The Fourth Doctor called the Master the "quintessence of evil" (TV: The Deadly Assassin) while Borusa told him that he was "one of the most evil and corrupt beings [that] Time Lord race [had] ever produced." (TV: The Five Doctors)

The Ninth Doctor described the Shadeys as "something evil". He mentioned to Rose Tyler that "Some people don't believe in evil... They say it's all subjective. No absolutes," and as a rebuttal to this, told Rose to "take a look" at the Shadeys. (COMIC: A Groatsworth of Wit)

Behind the scenes
The Universal Databank identified six types of evil which the Doctor has fought against. These were as follows:
 * 1) Those motivated by greed — Kal; Aydan, Eyesen and Kala; Forester; Bennett; Sevcheria; El Akir; Johnny Ringo; Grey; Samuel Pike; Theodore Maxtible; Maurice Caven; Dent; Irongron and Bloodaxe; Eckersley; Lupton; Kellman; Federico; Henry Palmerdale; the Usurians; Graff Vynda-K; Xanxia; Vivien Fay; Grendel; Adrasta; Tryst and Dymond; the Gaztaks; Rorvik; Morgus and Stotz; the Chief Officer, the Mentors; Kara; Doland; the Bannermen, Keillor; Peinforte;
 * 2) Misguided fanatics — Tegana; Tlotoxl; Maximilien Robespierre; Eric Klieg and Kaftan; Charles Carrington; Eric Stahlman; Hepesh; George Trenchard; Charles Grover; J. P. Kettlewell and Hilda Winters; Sorenson; Harrison Chase; Hieronymous; Taren Capel; Maximillian Stael; Kassia; George Hutchinson; Timanov; Dastari; Helen A;
 * 3) Those motivated by megalomania and/or a desire for conquest — the Master; the Rani; Borusa; Morbius; Animus; Eldrad; Meglos; Monarch; Mestor; the Borad; Kroagnon; Kane; the Ice Warriors; the Voord; the Drahvins; the Macra; the Dominators; the Krotons; the War Lords; the Nestene; Axos; the Zygons; the Kraals; the Krynoids; the Nucleus; the Movellans; the Nimon; the Terileptils; the Tractators; WOTAN; BOSS; Zaroff; Salamander; Tobias Vaughn; Magnus Greel; Morgaine; the Daleks; the Cybermen; the Sontarans;
 * 4) Those who seemed to be evil incarnate — the Celestial Toymaker; the Great Intelligence; Sutekh; the Mandragora Helix; the Fendahl; the Black Guardian; the Shadow; the King Vampire; the Mara; the Gods of Ragnarok; the Destroyer; Fenric;
 * 5) Those driven to become evil by a cruel twist of fate — Omega; the Wirrn; Xoanon; Scaroth; Mawdryn; Sharaz Jek; the Silurians and Sea Devils;
 * 6) Those motivated by factors beyond human notions of good and evil — the Dæmons; Kronos; the Xeraphin; the Eternals.