Iron Man became one of these during and after Civil War. This need not have happened; both sides were intended to have valid points, but the Editors failed to realise that some of the writers agreed with the Anti-Registration side, so they just kept penning atrocity after atrocity. The main book had Tony Stark (illegally) clone a god and set him on his former friends, resulting in the death of Bill Foster, aka Goliath. Moreover, the atrocities that didn't involve Iron Man, such as arresting Captain America for refusing to enforce something that isn't a law under the orders of someone who has no authority over him, also took place in the main book. It was a Knight Templar orgy from the beginning.
Foolkiller from Steve Gerber's Man-Thing believes that he's on Earth to punish fools for being insufficiently godly. At least the first one did. The problem is, a lot of people have held this identity since then, and while all of them targeted "fools" the definition of that term tended to be different for each of them.
The Punisher, Frank Castle, is one of the deadliest Vigilante Men in the entire Marvel Universe, with a body count that rivals most of Marvel's villains. His watchword is Pay Evil unto Evil, and when he's on one of his many vengeance sprees, the question is not "how far will he go?", but "how fast will he get there?" Notably, Frank doesn't believe he's on the side of the angels, and in several stories reflects on how his methods Pay Evil unto Evil.
The high-tech vigilante Cardiac targets people who commit evil and immoral acts, but find legal loopholes to escape justice. And let's face it; a lot of people would take Cardiac's side here. His victims are horrible men who rob people blind and cause innocents to suffer, but find ways to legally do it, always with selfish goals in mind. Even Spider-Man, who tries to stop him when he can, can't help but admire him a little sometimes.
Another notable admirer of Cardiac is none other than Otto Octavius, who met the vigilante while going through something of a Templar phase himself as the Superior Spider Man. Originally outraged when Cardiac stole one of his old inventions, Otto had a quick change of heart when he learned what Cardiac planned to use itfor, and the team-up produced what was arguably Otto's most redeeming Pet the Dog moment in the entire run.
The minor villain Demogoblin was a literal demon from Hell who was ironically a fanatical Christian determined to cleanse the world of sinners. However, his standards were so strict that only children were exempt from his wrath, and he considered everyone else to be sinners worthy of death.
Baron Zemo became one after his so-called reform in Thunderbolts. Zemo crafts elaborate plans to take over the world which he claims are actually to save it. Problem of course being they all still look and sound like an Evil Plan. This runs the mile of stealing power from nations he feels too stupid to wield them, making a machine to easily destroy all nuclear weapons, and lastly to instill himself with godlike powers to change the world for the better. This last one blows up in his face when his teammate betrays him in revenge and just plain not trusting him to actually mean the "for the better" part.
In Ultimate Fantastic Four, the Ultimate version of the Psycho Man mind controls a world to feel happy and content, while the Ultimate Silver Surfer argues that they are merely happy slaves. Also, Dr. Doom is always working on creating his "utopia", even if it means destroying the world as we know it. Hey, it's for a good cause.
The Ultimates (2015): Master Order, anthropomorphic personification of order, starts turning into one after Galactus attains his true purpose. Insisting this disrupts the status quo, Order tries forcing him to change back, and Galactus responds by punching his teeth out. The next time Order reappears, he's nursing a grudge, demanding Galactus change back, and when the Living Tribunal decides he doesn't have to, Order murders it, and merges with his brother Chaos to form a misshapen thing called Logos, which decides to start enforcing its idea of order on the universe by force. Galactus does try pointing out something is making Order act this way, but by the time he does it's a little too late.
The X-Men have faced the Purifiers; a sect of Christian fundamentalists led by Reverend William Stryker. The Purifiers believe that mutants are the children of Satan, and they are fighting a holy war against them.
Heel–Face Revolving Door aside, Magneto. He believes that mutants are being persecuted by regular humans, and that mutants are the future of mankind. He also believes a war between the two is inevitable, and intends to ensure the mutants will win.
Even more so Magneto's right-hand man Exodus, who gets bonus Templar points for being an actual knight templar during the Third Crusade. He's a particularly interesting case because his powers relate directly to his faith himself - or rather, his belief in his cause. When he has doubts/that faith is shaken, he gets chumped. When he is clear of purpose, he's a Person of Mass Destruction and borderline Physical God so powerful that it takes either the likes of Nate Grey or two entire teams of X-Men to bring him down (and even then, he won because it proved his point that they needed to work together). And when other people have faith in him... his powers start to multiply exponentially, to the point where one timeline has him as a Cosmic Entity so vast and so powerful that a Phoenix host is perched on his shoulder.
A lot of the mutant-hating human villains, who quite sincerely fear that the super-human mutants seek to replace humanity as the planet's dominant species. (It probably doesn't help that various mutant supervillains seem dead set on proving them right.) Some of them will go to extreme lengths to make the world safe for humanity. One good example is the semi-obscure villain Stephen Lang, who will calmly and seriously tell a young mutant girl to her face that he's sorry, but she has to die.
