All prisoners will be culled. Let the weak perish and the strong survive. This has always been the way of Apocalypse.The X-Men have faced many Villains over their long history, but several members of their Rogues Gallery stand out in terms of heinousness.
Examples from animated series can be found here.
- Apocalypse: An Ancient Egyptian who gained his powers from Celestial technology, En Sabah Nur ("The First One"), better known as Apocalypse, is one of the oldest, and one of the most evil, mutants in existence. Believing that the strong must dominate the weak, Apocalypse aims to test humanity. Those who survive the process will be allowed to live as his servants, those who fail, die. Apocalypse has a history of granting powers to other unscrupulous individuals, transforming Nathaniel Essex into the mad genetecist Mister Sinister (in exchange for Sinister agreeing to unleash a plague that would exterminate most of humanity), and empowering terrorist leader Moses Magnum, in exchange for the latter winnowing out the strong from the weak. His other crimes include, infecting the infant Cable with a technorganic virus, turning Cable's clone, Stryfe, into the monster he is today; trying to force humanity to reduce its own population by ninety percent or face the wrath of another metaplague; and effectively killilng Stryfe by bodyjacking him. That's without getting into the Bad Future, where he rules most of the world and has effectively run it into the ground, or the Age of Apocalypse timeline, where he devastated North America with nuclear weapons, reduced the human population by purges, and gave free reign to likeminded psychopaths Sinister, Holocaust, and Mikhail Rasputin, effectively destroying civilization. Believing wholeheartedly that those he considers weak must be slain, Apocalypse is well-deserving of his name.
- Fabian Cortez: This mutant, whose power could lead to Power Incontinence and Lethal Harmless Powers, was part of the defunct Upstarts, a group of rich, bored dilettante mutants that hunted and killed other mutants for points and bragging rights (the competition was set up by Selene to test possible recruits for the Hellfire Club). In his first outing, he puts together the Acolytes and seeks out Magneto in order to sway him back towards taking an antagonistic stance against humanity again. When Magneto is wounded, Cortez uses his own powers to seemingly help him, but in fact make him dependent on the "treatments" like a drug. His machinations lead to the U.S. and Russia destroying Asteroid M with a plasma cannon, and the deaths of his entire first group of Acolytes (including his own sister, which doesn’t bother him), whilst he flees with a triumphant smile on his face. When Magneto returns and Cortez loses his top spot in the Upstarts competition, he goes to Genosha and inspire the mutants there to rise up against their oppressive human government, causing a bloody civil war. At the same time, he kidnaps Magneto’s infant granddaughter (and replaces her with a shapeshifting mutant suicide bomber in an attempt to kill as many of the Avengers as possible) so he can use her as a Human Shield against her parents and grandfather, the X-Men, the Avengers, and Exodus. When Magneto is given rule of Genosha, he grants Cortez a place on his cabinet in exchange for regular rejuvenating treatments (Magneto’s powers are in decline at this time), but as soon as Magneto learns of hidden technology in Genosha that can restore his power levels again, Cortez predictably betrays him again by amping up ex-Acolytes to send against him. Not only an extreme mutant supremacist, a terrorist, a coward, a user, and a backstabber, Cortez committed his most despicable crimes to score points in a competition.
- Mister Sinister: A nineteenth-century eugenicist who believed that people should be bred in order to produce superhumans, Nathaniel Essex was approached by Apocalypse, who granted him near-immortality, regenerative, and psionic powers. Betraying Apocalypse, Sinister struck out on his own. Recognizing his own genetic handiwork in some of the Morloks, a group of street-dwelling mutants, Sinister hired the Marauders to exterminate them, because he viewed their existence as plagiarism. Obsessed with Scott Summers's bloodline, Sinister cloned Jean Grey, and sent the clone, Madelyne Pryor, to have a child with Scott, so that he might then steal the child. He later tried to use the High Evolutionary space station in order to alter the genetics of the entire planet; failing in this endeavor, Sinister later sent out the Marauders to murder everyone who knew about the dark future where Apocalypse ruled the world. On another occasion he merged with the Dreaming Celestial and transformed the entire population of San Francisco into clones of himself. At another time, Sinister, then part of the Weapon X project, promised to free the project's prisoners from the concentration camp they were held in, only to turn around and use them as part of his own experiments. Concerned only with his mad genetic theories, Sinister has worked with everyone from Josef Mengele to Apocalypse in the interest of furthering his research, and making himself the dominant life form on Earth.
- Omega Red: Arkady Gregorivich Rossovich was a Soviet soldier stationed at a small town who started murdering from sheer boredom. His fellow soldiers shot him in the back of the head when they caught him. The Russian government learned he survived and recommended him for the Soviet Super Soldier project, which he apparently only survived due to his nature. To survive carbonadium poisoning, he drains the life forces of those around him, even when a cure is available. He later turned on and killed several of his employers working for the Hand for the reason that they irritated him. In his presently final issue, he ends up in a regular Russian prison and taunts a prisoner dying of HIV/AIDS by calling him worthless. He later casually kills Wildchild by impaling him through the chest and dumping him in molten lava.
- Donald Pierce: The cyborg leader of the Reavers, he was a member of the Hellfire Club as the White Bishop for a time, but is really a psychotic, raving bigot who's also a Serial Killer of mutants. His hatred motivated him to turn people into Cyborgs to kill more mutants. Worst of all, Pierce knows if he goes after guys like Wolverine, Cyclops, Magneto, or Havok, he's going to get his ass kicked, so he targets baby and child mutants who can't fight back. Pierce is a vile, spiteful, cowardly bully so filled with hate, his last words before Cyclops kills him is to say he's just sorry he won't be around to see the Mutant Race destroyed. The one time he went after Wolverine it was with the help of Lady Deathstrike and the Reavers; they ambushed Wolverine, beat him down, then crucified him in the Australian desert and tortured him. If not for Jubilee, Logan would surely have died; as it was, the ordeal severely taxed his healing factor and screwed up his mental state for months of Comic-Book Time (but years of our time).
- Sabretooth: While Wolverine rejects the savage, animal side of him, another mutant embraces it. Victor Creed has reveled in his savagery ever since he was a boy, when his original origin story was that he killed and ate his parents. Sabretooth became a mercenary after, though he commits multiple murders for his own pleasure as well as profit. Sabretooth is known for making a game of hunting down women and children before killing and eating them, including live babies. One issue of Deadpool revealed that, after slaughtering a large group of people, he had a little girl locked in his closet as a snack for later. Sabretooth once joined X-Factor, though he was revealed to be faking a Heel-Face Turn in order to ensure that a psychic dependence on an addiction was removed. He promptly attempted to murder those he could. At one point, Sabretooth found himself as an unlikely father figure to Wolverine's amoral son Daken. This wasn't out of altruism however. Sabretooth played off Daken's desire for fatherly affection and drove him towarda confrontation with his father solely to hurt Wolverine more after he was forced to kill Daken. Every affection he ever had for Daken was a lie: Sabretooth would have killed Daken himself, but wanted the death to be at Wolverine's hands for maximum agony. For decades, Sabretooth has reveled in his monstrosity. He mixes his sadism with a brutal cunning and intellect, and is revealed to remember every life he's ever ended because he savors every death he deals.
- Selene: At times Black Queen of the Hellfire Club, she is one of the few mutants to be older than Apocalypse, and one of the few who can match his evil. A psychic vampire, Selene survives by draining the minds of other beings into herself, a move which brainwashes those she only preys on a little, and kills those she drains completely. She's also possessed of a phenomenal god complex, and has repeatedly tried to attain godhood, and has forced others to worship her. Her crimes include trying to psychically devour the entire city of Rome; using mind control to force the citizens of Nova Roma to worship her as a goddess; trying to kill her own descendant, Magma; successfully killing her loyal servant Eli Bard; manipulating Wither, an otherwise good kid, into descending into omnicidal mania while pretending to love him; promising the Upstarts prizes if they committed enough murders;repeatedly trying to bodyjack Rachel Summers; and enslaving the souls of all Genosha's dead. A seemingly immortal parasite, Selene set the standard for all future Queens of the Hellfire Club to follow.
- Shadow King: Storm’s Arch-Enemy, Amahl Farouk was a powerful mutant who made his living as a crime lord, using children (including Storm) as pickpockets or prostitutes. After being defeated by Charles Xavier and locked in the astral plane, he became far worse. Taking the alias "The Shadow King," Farouk became a being of psychic malice. Not content to remain on the astral plane, Farouk consistently possesses others with psychic energy, and then enacts a game of destroying them mentally. He often forces them to indulge in the sickest desires he can imagine, or that he finds in their subconscious, leaving them aware that they are doing such horrible things, but making them enjoy it. Farouk enjoys psychic torture as a hobby, and seeks to corrupt the hearts and minds of every human he can, this being both an art and enjoyable past time to him. Recently, Farouk was the one to reveal to the young boy who might grow to be Apocalypse that his life was a lie and he was the destined destroyer. Being Farouk, he mocked him the entire time about how his life was a worthless simulation, and showed utter glee in awakening the one to commit genocide on humanity.
- Reverend William Stryker is the founder of the Purifiers, an organization of religious fanatics who believe mutants are an affront to God. Their first appearance opens with them gunning down a nine-year-old girl and eleven-year-old boy. Stryker's crusade began when he killed his baby mutant son, and then broke his wife's neck for giving birth to a "monster." He tries to brainwash Professor Xavier so he'll kill every mutant on the planet, and murders his second-in-command when it becomes clear she has the mutant gene. He also tries to kill Kitty Pryde on live TV, but is stopped by his guards.
- While Wolverine has clashed with several of the above, including Omega Red, Donald Pierce, and especially Arch-Enemy Sabretooth, he also has his own villains.
- The Founder is the Big Bad of Jason Aaron's run. In the 1920s, The Founder was the young son of a notorious robber-baron whose workers went on strike, leading to the father bringing in thugs from the Pinkertons to control the strike, killing many workers; leading to the workers hiring Wolverine to fight the thugs; leading to the robber-baron murdering the head of the union; leading to Wolverine killing the robber-baron, whose son swore revenge and dedicated the rest of his life to learning everything, everything about Wolverine. Over the years he recruited many others with perceived or real grievances against Logan, forming the cult called the Red Right Hand. When a member tried to leave the group, he forced her to smother to death a helpless old woman (Sabretooth's mother, as it turns out). In the modern day the Founder, now an old man, decided to act against Wolverine personally. He and the other members sold their souls to the hell-lord Marduk Kurios, in return for damning Wolverine to Hell and allowing a demon to possess his body. They then let the demon and their bodyguards, the Mongrels, loose on anyone who had ever been kind to Logan, ever (killing John Wraith, Silver Samurai, and temporarily, Mystique). Once Wolverine got out of Hell and back into his body, he chased after the Founder and the Red Right Hand, killing the Mongrels along the way, only to find that the cult had already committed suicide. The Founder left a tape-recorded confession for Wolverine, though, in which he revealed that he never intended Wolverine to die, but he wanted him to win, since the Mongrels were Wolverine’s long-forgotten illegitimate children. Even though Wolverine defeated his enemies, the bad guy decidedly won. In the narration for his flashback (provided by him), he mentioned how much he enjoyed what an evil man his father was. To him, the ability to brutalize others is a sign that a person is "strong."
- Tomi Shishido, the Gorgon, fully lives up to his name by turning people (especially girls) into living statues, which he uses for decoration. His villainous career started very early, when he founded the "Dawn of the White Light," a mutant surpremacy group which put even the Brotherhood to shame. At the age of 18, he slaughtered his entire family in order to prove himself worthy of joining the Hand. His most heinous act was when he brainwashed Wolverine into a servant of HYDRA and sent him on a brutal killing spree, which caused several dozen innocent deaths, among them the Hornet and Northstar, which haunts Logan to the present day. He also has absolutely no problems with killing children, which he showed when murdering Phobos.
- From the Wolverine: The Best There Is limited series comes the enigmatic Mr. Winsor, alias Contagion. Born from a Latverian eugenics program, Winsor's body contained every single disease known to man, which he trained himself to be able to release at will. Killing all the other children born from the program, Winsor struck out on his own, acquiring the services of numerous nearly-immortal individuals as both enforcers and test subjects, whom he would infect over and over again with his diseases in order to make them stronger and more deadly. Winsor used his abused son, deformed from exposure to his father's diseases, as bait to acquire Wolverine for his experiments under pretense of wanting to use his research to cure his son's condition, knowing Logan, as a Friend to All Children, would never refuse the offer. Ultimately, however, he revealed his true motive: in making his diseases stronger and stronger he hoped to engineer one that could kill absolutely anything, which he would then unleash on the world and then the entire universe via a stolen spaceship. When his followers ceased being useful, he subjected then to And I Must Scream to ensure they would not rebel. With evil plans unmatched in scale for an Earth-based villain, Contagion more than makes up for his brief tenure in the comics with his cruelty.
- Dark Beast, the Evil Counterpart of the kind-hearted Hank (Beast) McCoy, is a Mad Scientist who hails from the Age of Apocalypse. Initially the Bastard Understudy of Mr. Sinister, Dark Beast earned a reputation as a sadistic monster in Apocalypse's concentration camps for his cruel experiments which tortured and killed many, giving him the nickname of "Beast," which he liked enough to mutate himself to better fit the moniker. When Dark Beast was brought to the X-Men's world he set about killing everyone the good Beast cared for that he could and continued his monstrous experiments on innocents. With his most heinous actions being to create a machine that fed off Hank's lifeforce while keeping him in unspeakable agony, in addition to his experiments on children, Dark Beast eventually attempted to foster a war between the X-Men and S.H.I.E.L.D.. When exposed and dying from experimenting on himself, Dark Beast attempted to initiate a bomb to take the X-Men with him simply out of spite.
- Ultimate X-Men: Magneto is very different from his usual Noble Demon status. First of all, although Retcon gave him his more familiar background, originally Ultimate Magneto came from a wealthy American family and was never on the receiving end of a genocide or any sort of prejudice, meaning initially he didn't even a Freudian Excuse for his actions and was even more arrogant note . No Well-Intentioned Extremist Anti-Villain as the mainstream one is, Ultimate Magneto is an abusive parent who once broke his own son's legs for challenging him; is a true mutant supremacist who believes that mutants should replace humanity rather than merely be protected from them (in fact, he's even implied to have been eating humans at different points); and has, on several occasions, attempted to eradicate the human race and rule over a post-apocalyptic mutant utopia in the aftermath as an extension of this creed. He is savagely ruthless to his enemies and, here, is the one who crippled Charles Xavier, because the latter had started to realize he was insane. He rules the Brotherhood of Mutants like a cult and encourages them to murder as many humans as possible, children included, and has organized several terrorist attacks with high body counts.
- X-23: Dr. Zander Rice, one of the lead scientists of Weapon X's X-23 project, has X-23 kept in a padded room except during training sessions or assassination missions, almost kills her with radiation poisoning to trigger her healing factor at the age of seven, and surgically removes her natural claws one at a time, coats them with adamantium, then re-implants them-all of this without anaesthesia-at the same age. He develops a pheromone "trigger" that activates her berserker rage and uses it to get X-23 to kill her martial arts instructor, and leaves her behind on a mission to be killed after he murders the other members of the team so he can claim they were taking fire and had to retreat. After X-23 shows back up alive, Rice then manipulates the head of the X-23 project, who had raised Rice after his father's death, into granting Rice control of the project, at which point Rice then sends X-23 to kill the man, his wife, and son - even though Rice knows the boy is his own son, from an affair between Rice and the wife before her marriage (X-23 leaves the child alive). Upon taking over the project, he begins the development of embryos X-24 through X-50, which he intends to sell to the highest bidders, and then taints the one remaining person X-23 cares about, the project scientist who was her surrogate mother, with the trigger pheromone, which causes X-23 to fatally injure the woman - just as she was about to take X-23 and disappear after destroying the project complex. Rice's reasoning for all of this is that his father, who worked on the original (Wolverine) Weapon X project was killed by Wolverine when he escaped, and Rice held X-23, who is Logan's genetic double, responsible for Wolverine's killing of his father.
- Generation X: Johnston Coffin, featured in four obscure issues, is wanted by S.H.I.E.L.D. for crimes against humanity, but instead somehow finds himself employed by the US Government. With the government's blessing, he builds a Hellhole Prison where he "fixes" disobedient teenagers, many of which had only said or thought something disobedient. What really puts him over the line, though, are his "Special Children" - kids from his first Hellhole Prison in the '70s, whom he's wired up to huge cyborg bodies and uses as security. They've been that way so long, it's implied in perpetual agony, that their bodies have actually begun to rot. He also has half a human mounted on his wall, is implied to be a rapist, and carries around the skull of a child he shot in the head everywhere he goes.
- X-Men: First Class: Klaus Schmidt, a.k.a. Sebastian Shaw, is a diabolical mutant supremacist who believes humans to be inferior to mutants. As a Nazi Mad Scientist, he used his position to try to find "gifted" mutants, and upon finding a younger Erik Lensherr, he killed his mother after Erik failed to impress him with his powers, solely to motivate him, before subjecting Erik to horrible experiments. After the war, he adopts the Shaw identity and ingratiates himself to high ranking members of the government with his Hellfire Club, manipulating Russia and America alike. Shaw assaults a CIA facility, murdering every agent within, and when one of the young mutants stands up to him, Shaw, despite his creed of "not harming his own kind," murders him without hesitation and barely concealed enjoyment. Shaw's ultimate goal was to push Russia and America into nuclear war, allowing mutant-kind to thrive in the aftermath and creating a kingdom of mutants that he himself would rule. Even when thwarted, Shaw planned to absorb all the nuclear radiation in his atomic sub and unleash it upon Cuba to destroy it personally and trigger atomic war.