Megatron from Beast Machines willed the establishment of total order by eradicating free will. After conquering Cybertron by disabling the Transformer population, he extracted every single one of their sparks and stored them away. He intended to absorb every spark into his consciousness to create a perfect, technologically precise entity.
This seems unusually unpleasant even for Megatron, yeees.
In "Mr. Sandman, Dream Me a Dream", the titular creature seeks to end war - by making the entire human race sleep for 500 years.
In "Ragnarok and Roll", a depressed young man with a broken heart decides to end human suffering - by using a magic flute to play a "song of destruction" that will end the world.
Most of the Superman: The Animated Series episode "Brave New Metropolis" takes place in a Mirror Universe where Lois Lane's death has turned Superman into a tyrant who cooperates with Lex Luthor. Obviously, this causes the line "It is forbidden to interfere with human history" from the movie to become Harsher in Hindsight. Though this could be a bit of a subversion as Superman truly thought he was doing good because Lex was lying to him and purposely got rid of people that could have told him different. When Lois shows Superman the truth he is very ticked.
The two-part Justice League adventure "A Better World" featured a vaguely similar plot to the above. It featured the League's Mirror Universe equivalents, the Well Intentioned Extremists called the Justice Lords, who decided to end crime by ruling their world as fascist dictators. Interestingly, in this version, the straw that broke the camel's back was Superman killing Luthor, in response to his murder of the Flash. The aftermath of this encounter was seen in the first two seasons of Justice League Unlimited.
In the Justice League Unlimited episode "Patriot Act", General Wade Eiling takes a Super Serum in order to take out Superman, as he feels metahumans, aliens, and any other powered being on Earth is a threat to humanity. Unfortunately, Supes is off planet and confronts a group of leaguers that technically have no powers: Stargirl, STRIPE, Shining Knight, Vigilante, Green Arrow, and later the Crimson Avenger and Speedy.
Superman: Doomsday had Superman's clone turn into this. He's obsessed with protecting Metropolis but decides that he should have the final word on how it's protected, leading him to brutally slaughter Toyman for the murder of a 4-year-old girl.
The Darkwing Duck episode "Time and Punishment" has Gosalyn get stuck on Quackerjack's Time Top and transported into a Bad Future, where in the years she had been absent Darkwing went through a period of Heroic B.S.O.D. after thinking Gosalyn had run away, then eventually snapped out of it when he decided to devote himself entirely to crimefighting. He took it way too far, becoming a tyrant named Darkwarrior Duck who had run every supervillain out of St. Canard and then started punishing people severely for "crimes" such as staying out too late and eating too much junk food.
Goliath, when he used the Eye of Odin to protect Elisa and Angela. The Eye amplifies strongest personality traits of any mortal that uses its powers without protection; quickly warping Goliath's normal protective guardian nature into an obsession with controlling those he cared for and destroying anything that could possibly threaten them. When they complained that the eye was making him crazy, he got pissed. Once it was removed, he reverted back to normal and was horrified at how far he almost went.
The Hunters and the Quarrymen may have started out as He Who Fights Monsters, but they turned into genocidal villains. It's understandable if they want to kill Demona, who's trying to wipe out humanity, but they want to kill all the innocent gargoyles, too. To give you an idea of just how bad this is, in the episode that introduced the Hunters, one of them, presumably a rookie, questioned the Hunters' desire to kill all Gargoyles, stating that Demona was their group's original target. One of the other Hunters grabs him by the throat and threatens to kill him for even suggesting that any Gargoyle deserves to live.
Those two hunters? They're brothers.
And back on the Quarrymen, gargoyles weren't their only victims. They brutally attacked a group of peaceful gargoyle activists and sent what's left of it to the emergency room.
Ultra Magnus in Transformers Animated, who is perfectly willing to suppress the truth in order to maintain order. He also urges his subordinates to do the same.
General Crozier from Metalocalypse, at least until Mr. Salacia took over his mind in the Season Two finale.
South Park has thrown this label around on a number of occasions, sometime becoming rather insufferable with it.
Cartman especially exhibited this in the Coon and Friends episode, destroying all that annoyed him with Cthulhu.
The Coon: I'm going around making the world a better place!
Mysterion: For you! You're making it a better place for you!
The Coon: Right, that's what superheroes do.
The Knights of Standards and Practices in "It Hits The Fan". Granted, they were somewhat justified because cursewords were curse words and "shit" was causing an epidemic, but they seemed fine with killing people who were not the masterminds behind this incident.
In the movie, Kyle's mom is this, although she starts a war, a genocide against Canadians, and nearly causes Armageddon all in the name of cleaning up the entertainment industry.
Al Gore in "ManBearPig". When he floods Cave of the Winds, he takes pride in hearing that he probably just killed 4 children, since it means he killedManBearPig.
Kyle himself is gradually leaning towards this trope in his rivalry with Cartman, some of their conflicts have shown his willingness to outright kill him (in Fat Beard for example, he attempts to convince Cartman to travel to Somalia in his ill-defined plan to become a pirate, he is later seen gloating about assisting in Cartman's supposed death, unfazed by the fact that Butters, Clyde and Kevin went along with him, Ike joining, however, is enough to change his mind.
Rob Reiner is portrayed as an arrogant wealthy liberal who eats vast and unhealthy amounts of junk food, yet still harasses people who smoke in "Butt Out". The tobacco company he attacks is shown to have a nice executive and happy workers, and in contrast, Rob Reiner is a terrorist with creepy followers who tried to kill Cartman.
Fire Lord Sozin could be considered this because he wanted to conquer the other nations for their own good.
WanShiTong, the Spirit of the Library, only allows Team Avatar into his library if they swear that they are only seeking knowledge for knowledge's sake, not for military purposes. Horror ensues when he attempts to trap them in his library eternally after discovering that they've broken their word.
The Equalists from the Sequel Series, The Legend of Korra. Their quest for equality for non-benders is realized through terrorism and what amounts to soul rape.
Tarrlok also counts, responding to the Equalist threat by setting curfews against non-benders and arresting any who complain. People are also arrested simply for having associated with Equalists.
Possibly subverted. Tarrlok indicated that his main goal in enacting the curfews was to play the Equalist-Republic City conflict for more personal power.
Unalaq from Book 2 of Korra, a religious fanatic that seeks to unite mankind with the spirits. By fusing with the God of Evil, that is.
Kuvira from Book 4 seeks to reunite the Earth Kingdom after the Red Lotus threw it into chaos by killing the Earth Queen. Her primary method is to bully state governors into sacrificing their resources and swearing loyalty to her, and sending those that disagree with her off to "Re-Education Camps". Eventually, she decides that the Royal Brat she's working for is not proper leadership material, so she publicly usurps him, declares herself Emperor, and vows to crush anyone who says otherwise, to much applause.
Mr Krabs of Spongebob Squarepants is determined to punish his rival Plankton for his unscrupulous deeds, even when he is using perfectly legitimate methods. Taken to extremes in "Plankton's Regular", where Plankton finally gains one regular customer and offers to call a truce with Krabs in return for keeping him. Krabs immediately becomes obsessed with taking away said customer. And that's not to mention the fact that Mr. Krabs often takes offense when Plankton simply isn't completely miserable and often goes out of his way to ruin Plankton's life For the Evulz.
Crossed the Moral Event Horizon in One Coarse Meal. Not only did he spend the whole episode torturing and terrorizing Plankton for no other reason then for petty kicks, but when Plankton attempts suicide because of him, he just laughs and even erases a picture of him, which could imply that it was his plan all along. Made even more teeth-grinding in that he gets absolutely no comeuppance in the end. Not a trace.
Mr Krabs in general has become so over-the-top evil from his original "greedy-but-likable-boss" status that even the creator of Spongebob, Stephen Hillenburg, deemed Mr Krabs just as evil as, if not worse than, Plankton himself.
In Futurama, a robotic Santa Claus has been programmed to determine who is naughty and who is nice. Unfortunately, his standards for nice are set too high - everyone except Dr. Zoidberg is considered naughty, and to make matters worse, he ain't limited to putting coal in your stocking. He's more likely to turn you to charcoal instead.
Ben himself almost becomes this after getting the Ascalon Sword from George and Diagon's powers from Vilgax, Vilgax pointing out he could eradicate evil by his mere will now. He is eventually stopped from doing it by Julie.
The Big Bad in the season 3 finale of Archer is determined to colonize Mars, even if that means kidnapping, slavery and hijacking, because he thinks it's the only way to save humanity.
Starlight Glimmer prior to her reformation in My Little Pony: Friendship Is Magic. After losing her only childhood friend because of him getting a cutie mark, she develops a worldview in which cutie marks (which are supposed to signify one's special talent) are essentially harmful and lead to dissaray. This results in her founding a village where she takes away every pony's cutie marks, making them "equal" and brainwashing everyone who shows signs of dissidence. Ironically, she keeps her own cutie mark, because without that she wouldn't be able to "create equality". When her perfect society is ruined by main heroes, she goes as far as travelling back in time to make sure that Twilight never meets her friends and they never get in Starlight's way. What's interesting though is that the main driving force behind Starlight's actions seem to be not cutie marks themselves, but her own loneliness and unwilingness to restore older friendships. So she does sincerely believe she's in the right, but deep inside she's still unhappy because, despite all her efforts, she doesn't have any actual friends. This becomes the key to her eventual Heel–Face Turn.