'"There are some corners of the universe that have bred the most terrible things. Things that act against everything we believe in. They must be fought."
— The Second Doctor
Davros, the Mad Scientist creator of the Daleks was a crippled scientist on a planet with two races locked in civil war. To win, Davros created the Daleks: powerful, murderous creatures that could feel only hate and rage for every other species. To finalize the Daleks, when his superiors were about to cancel his immoral research, Davros engineered their extinction. Davros would return many times, improving his Daleks to wipe out or subjugate all other life with himself at their head and achieved the extermination of countless life forms. When he returned in modern times, Davros unleashed them on earth, revealing a new objective: to cause a massive chain reaction with a Reality Bomb that would result in: " People and planets and stars will become dust. And the dust will become atoms and the atoms will become... nothing." Davros gleefully declared his ultimate objective to be no less than THE DESTRUCTION! OF REALITY! ITSELF! A man who has admitted he would unleash a virus to end all life solely because he could, Davros is a man who seeks power that will put him above the Gods and has remained one of the Doctor's most evil and tenacious foes.
John Lumic, the creator of the Cybermen. A Corrupt Corporate Executive and coldblooded, amoral snake of a man who was suffering from a terminal illness. To discover a path to immortality, Lumic had homeless people abducted and experimented upon to convert them into Cybermen, leaving their human brains trapped in robot bodies, forced to act to their programming. When the British Government refused to bankroll Lumic's project, he decided to overthrow it by dispatching a horde of Cybermen to liquidate any potential dissidents to his rule, intending to eventually spread them across the globe.
The Master is seen as the Arch-Enemy of the Doctor for a very good reason...
The Roger Delgado incarnation is the epitome of Faux Affably Evil and was often quite helpful to the Doctor if it served his purposes. He is also a petty, spiteful, murderous megalomaniac who values nothing more than power and angering the Doctor. Indeed, he admits in "The Sea Devils" that the only reason he's helping the eponymous creatures Kill All Humans is because the Doctor is fond of humans. Afterwards, at the end of his final regeneration and at the brink of death, he values nothing more than survival. Species, planets, even whole sections of the universe; there is no limit to what he will destroy to survive. And he finally achieves this by killing and hijacking the body of Tremas, quite probably the friendliest and most helpful person the Doctor has ever met who wasn't one of his companions (and thereby forcing the Doctor to look at the face of a murdered friend every time he fights him from then on).
The resultant Anthony Ainley incarnation lacked any sort of foresight or consideration for the consequences of his actions, and, in a way, that made him even more dangerous. His first appearance has him accidentally obliterate approximately a quarter of the entire universe and go on to cause further death and destruction almost for the sheer fun of it. This incarnation of The Master was far less reserved, murdering any in his way and treating their deaths with a cool, amused disdain. Even the extermination of countless billions was nothing more than a pebble in the Master's path.
The John Simm incarnation reaches new heights in the level of childish glee he experiences from mayhem and death. After conquering the Earth (the planet got better), his first action is to, for no reason whatsoever, order the execution of a tenth of the population, proceeds to rule a horribly and needlessly brutal regime, forcing his prisoners to watch while he incinerates the Islands of Japan just for fun, mistreating his servants, and beating his wife and ultimately aspiring to conquer the whole of time and space, and the only reason he refrains from enacting a Kill 'em All ending is because he would also die. Even when dying after his abused wife shot him, the Master refused to regenerate, relishing the agony he caused The Doctor in leaving him the final Time Lord. His final words were a cold declaration: "I win."
Rassilon, the once proud leader of the Time Lords. After he became twisted, Rassilon sought immortality and power at the expense of all reality and everything that lived. Rassilon was the one responsible for the Master's madness, hoping to use him as an eventual pawn. Over the course of the Time War between Time Lords and Daleks, Rassilon opted for a final solution: to wipe out all of space and time so the time Lords would remain as pure consciousness, yoked to his will because he didn't see any other way to end it. Making things worse he kills unnamed Timelord for suggesting that they allow the Doctor to wipe out Gallifray and end the Time War for the good of the rest of the universe and all that are suffering in it, because he doesn't want to die. Even in the past, Rassilon had showed a predilection for 'cleansing' lesser species and knows his actions will release a varieties of evil and demonic forces that had been locked away after the Time War without a care in the universe.
The Marshal from "The Mutants" is a petty tyrant who nevertheless stands out in depravity. A ruthless colonial overlord who reigns over a planet of mutants, The Marshal hunts the poor natives for sport, gloating how pathetic, disgusting and diseased they are. On learning the humans are turning the planet back over to the natives, leaving him without his position of power, he arranges the murder of the only man who knows this and attempts to wipe out the planet's entire population in order for it to be repopulated by human colonists with him as their ruler.
House, the sentient Asteroid "The Doctor's Wife" is a creature that has butchered hundreds of Time Lords unlucky enough to land on his surface and stitched their bodies into subservient playthings (also took over the mind of an Ood to act as a servant), then hijacked the TARDIS for use as a new body, leaving the Doctor behind to die on the collapsing remains of his old body - and condemning its playthings to die without his influence, to boot. House then decides to use the Doctor's companions Amy and Rory as its new toys, forcing them into the labyrinth of the TARDIS corridors, torturing the two of them with nightmarish illusions, and taunting them with its catchphrase : "Why shouldn't I just kill you now?" House is a being that operates solely according to its sadistic principles of amusement and enjoys torturing whoever is unlucky enough to fall into its grasp. Death might be certain, but House makes certain that when the end comes, its victims will wish for death.
Xanxia from "The Pirate Planet" is a supposedly dead queen of Zanak who was so brutal and cruel, that she is feared in legend long after her demise. To rejuvenate herself, she manipulated a Noble Demon called The Captain into wiping out entire populated worlds so she can take every scrap of mineral and material from them so she could keep her body young, beautiful and immortal.
Sutekh from "Pyramids Of Mars" is an Omnicidal Maniac and sadistic monster who desires nothing less than the extermination of all that lives solely so that it cannot challenge him. Once the security chief of the Osirian race, Sutekh grew so paranoid he even had his own loyal people slaughtered by his monster followers which forced the remaining Osirians to band together and seal him away. Upon release, Sutekh planned to use his immense power to exterminate all that lived, knowing not even the Time Lords could challenge his immense power.
The Great Intelligence gained a true form solely by harvesting the souls of living beings. It followed this by conquering its world. The Great Intelligence practices a cruel form of destruction on people: manipulating their lives since childhood until it throws their lives away for its own benefit. The Great Intelligence makes a final attempt to utterly break the Doctor by personally undoing every single victory he had ever won and destroying every friendship he had ever made by infecting every moment of the Doctor's lifetime, and forces him to feel this happening to him as he does so, even though this would be fatal to the Great Intelligence as well. The reason? Spite at the Doctor preventing its victory.
Mrs Gillyflower from "The Crimson Horror" makes an attempt to wipe out all humanity so she and her 'perfect' chosen people can create a new Eden. She refuses a place for her own daughter Ada because Ada is blind and doesn't fit with Mrs. Gillyflower's version of perfection, knowing this condemns her daughter to death. The kicker to this is she blinded Ada herself by experimenting on her with deadly poison to prolong her own life, revealing her as nothing more than a nasty hypocrite and Smug Snake who was willing to let everyone on earth die so she could live out her fantasies of perfection.
Koquillion from "The Rescue", also known as Bennett. To cover up a murder he committed, Koquillon murdered everyone on his ship, before wiping out the population of the peaceful planet Dido, unintentionally leaving only two survivors. blames the locals for killing the people to the only other survivor Vicki, whose father was killed. He disguises himself as Koquillion to convince Vicki of his story, and when the Rescue Ship came he wanted to convince the authorities to destroy the planet to removing all traces of his crime. The Doctor showed nothing less than utter disgust at all this, declaring "you destroyed a whole planet just to save your own skin."
The 456 are Starfish Aliens who incorporate prepubescent human children into their physiology, keeping them eternally alive, childlike, and fully aware, because their bodies produce hormones that act as euphoric drugs on them. One child has been a human reefer for over 40 years, turning him thin, hairless and immobile. They are bargaining to take 10% of the world's children to use as drugs or else they Kill All Humans, and they would almost certainly have been back for more later.
Prime Minister Green calmly allows 10% of the world's children to be sold as narcotics. He orders Frobisher, the man who's been most loyal to him, to give up his own children just to make the cover story he's created realistic. This leads him to shoot his family and himself to spare them the horror. After all the horror and pain, Green's first thought is how he can blame the Americans.
Oswald Danes from Miracle Day, a convicted child rapist and killer whose defense in court was "she should have run faster." After surviving his execution due to becoming immortal (along with everyone else on Earth), he starts playing the media for forgiveness and seems well on his way to becoming a Dark Messiah. On top of that, throughout the season, it's implied that he does have some guilt over what he did and wants to die — then the finale shows that these Death Seeker qualities actually make him more of a monster, not less. Why? Because he seems to believe that when he dies, he'll be able to torture his previous victim forever in Hell — in fact, his last words are to yell out that he's coming for her and that she should start running.
The Dalek Time Controller repeatedly proves to be one, having a cold, calm, and calculating personality that sets him aside from his Dalek underlings and being the true power in charge of the Dalek conquests and implicitly the Time War, which coupled with his sadistic attempts to break the Doctor in "To The Death" by forcing him to watch all life on earth die before killing him lead to the otherwise kindhearted and casual Doctor furiously vowing to exterminate the Daleks from creation if he ever get.
The president of the English Empire Nigel Rochester in "Jubilee" is one of the more disturbing villains in the Big Finish series, being a Dalek worshipping human in charge of a nightmarishly genocidal and xenophobic empire which attempts to emulate the Daleks in all the worst ways, while remaining cheerfully upbeat and affable even when mutilating midgets to fit in his "toy Daleks" or beating his wife for speaking in contractions. The fact hes voiced by MartinJarvis make him all the creepier.
Wendle Marr from the much-maligned "Nekromanteia" happens to be the most despicable and unlikable character from a cast made up entirely of despicable and unlikable characters. He starts off the play by sending a fleet of ships and their crew to their deaths, then has the gall to order the flagship's commander to die as per his company's protocol. When the guy refuses, he has his assistant prepare to destroy the guy's livelihood and the lives of his family. He later receives funds to help improve the horrid quality of life for the workers on his pet project, but decides to instead pocket the money for himself and kill all the workers once it is finished. He is so evil that even the aforementioned ship commander (who tries to rape companion Erimem) is more likable than him, with his assistant killing him and making the ship commander CEO of the company instead after his greed nearly causes the destruction of the whole universe. Seriously, TheDaleks have done more good for the universe than Wendle Marr.