"Imagine. I now possess the power to end hunger. To abolish disease. To eliminate crime. To establish a perfectly content, perfectly ordered world - all under the benevolence of MY IRON WILL!" - Doctor Doom
Buffy Season Eight reveals that all of Angel's actions as Twilight (including being the head of an anti-Slayer military organization and putting Buffy and her crew through all sorts of hell) were all to prevent anything like the Fall of Los Angeles (as detailed in IDW's After the Fall) from happening to the entire Earth. Of course, the higher being that convinced him to do so had also duped him into thinking it was good when it wasn't.
Likewise, both Buffy Season Eight and Angel and Faith feature Whistler as one, first with his involvement in the Twilight apocalypse (which he freely admits to Angel would have resulted in the deaths of at least two billion people), and later his plan to "evolve" the world with a magic plague. Despite the heavy casuality risk in both plans, Whistler truly believes that what he's doing is necessary to preserve the Balance Between Good and Evil and save the world. Angel is actually sympathetic to his cause in the latter, but simply refuses to help him harm any more innocents or cause any more collateral damage than he has already.
Ra's Al-Ghul's intention in the Batman comics (and Batman: The Animated Series) was to stop mankind's destruction of the environment. This could be accomplished by wiping out roughly 2 billion people. In the movie Batman Begins, he attempts to make Gotham an example of crime and decadence in order for the world to see its horror.
Bioterrorist Poison Ivy wants plants to be respected. It's the "and completely dominant" part that causes trouble.
Magneto in X-Men is one of the archetypal examples in the medium. He wants peace and safety for mutantkind—but he's willing to achieve it at the expense of humanity at large. Magneto's characterization varies wildly depending on who is writing him, but the most influential version is the one envisioned by Chris Claremont and fits this trope to a tee.
Cyclops took this role after the events of Avengers vs X-Men, having killed Professor X and dedicated himself to starting a new Mutant revolution. He's been explicitly compared to Magneto by both supporters and detractors — which is more than a little comical since a reformed Magneto is a member of Cyclops' team of rogue X-Men.
Dr. Bolivar Trask, the renowned anthropologist, became an early X-Men villain when he publicly voiced his fears that superhuman mutants might take over the world and enslave humanity. Considering what mutant supervillains have been up to before and since in the Marvelverse, it's not quite fair to say that he was entirely wrong. Nevertheless, his proposed solution — To launch an army of Sentinel robots to contain and neutralize the mutants — qualifies him for this list.
Trask's son Lawrence basically continued his father's plans, with the added motive of revenge for his father's death. Later, government scientist Steven Lang launched an operation similar to Trask's, for much the same reasons.
Arguably, most human X-Men villains qualify, as they're basically Magneto in reverse: Ordinary humans looking after human interests and not wanting to be dominated or exterminated like rats by a super-powered caste of mutant overlords. (Which has actually happened or nearly happened a number of times in the comics over the years.) Though like the mutant supervillains, some are less "well-intentioned" and more "extreme" than others, and vice versa.
Spider-Man's enemy, the Vulture, is a good example of the other type of this trope. Many years after his debut, he was given a backstory in which an unscrupulous business partner cheated him out of the proceeds from his inventions. He wrecked said partner's business, stole back his money, and discovered that he enjoyed the thrill. Eventually, the partner surfaced, and the usually not-murderous Vulture went after him; Spidey stopped the Vulture but taped the partner's confession.
Spider-Man has often fought a high-tech Knight Templar called Cardiac who targets people who commit evil and immoral acts, but find legal loopholes to ecape 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.
Cinderella's fairy godmother, as well as Geppetto, in Fables embodies this trope. The fairy godmother just wanted people to be happy, and Geppetto didn't start out intending to conquer the world.
Grant Morrison's Marvel Boy is a good example of this. The miniseries' alien protagonist, the extradimensional Kree, Noh-Varr, has his ship shot down and the rest of his crew killed by a supervillain that wants to make a profit off of his technology and dissected remains. As such, he winds up understandably pissed at the human race (to the extent that he knocks down buildings to spell out "F#$k you" to the human race in letters several blocks high, though he herds the inhabitants away so there will be no casualties). Noh-Varr finds Earth's social ills to be ridiculous and unreasonable and intends to make war on Earth and "terraform" it to be like his home planet, Hala. He would be a classic Villain Protagonist, but genuinely does seem to believe that what he's doing will better Earth for its inhabitants.
Norman Osborn during the Dark Reign saga saw himself as this, as we see in his "monologue" at the end of Siege. He says that his idea was to make a safer world by not letting just anyone put on a costume and decide to save the world by themselves, since they would end up causing more harm than good, knowing that, someday, the mutants would turn against mankind, or the Hulk would snap and go on a rampage that could kill millions. And he used the Superhuman Registration Act in his attempt, since it would be the perfect excuse - whoever was against him was automatically labeled as "non-sanctioned" and hunted down.
Professor Fairfax in Paperinik New Adventures. The problem: as the years go on, overpopulation and dwindling natural resources will become more and more of a problem. The solution: using earthquake machines to raise a large section of the Pacific Plate above sea level, freeing up space for new cities and farms. Never mind that the ensuing earthquakes and floods will all but wiped out the entire west coast of the United States. As one character puts it: "If you think about it, his plan isn't illogical at all: he's simply willing to kill millions of people to give billions of people a better future."
Rayek in ElfQuest claims to want what's best for all of elfkind, but is also convinced that he's the only one who knows what's best for them, in spite of all arguments to the contrary. This comes to a head when, in an attempt to correct a Time Paradox, Rayek takes Leetah, Skywise, Ember, Suntop, and Picknose and his family ten thousand years into the future in the Palace - leaving Cutter and the rest of the Wolfriders stranded in the present.
Winowill starts out as one of these. She just wants to keep all the "real" elves nice and safe, even if it means keeping them locked in perpetual stasis and committing genocide on the Wolf Riders. Later, she just becomes plain out and out Ax-Crazy evil.
The major turning point seems to be the time she drove her own son insane in order to cover up the murder of her troll lover. After that, there were no limits to what she'd stoop to.
Watchmen: A very spoilerish example, but: Ozymandias? Possibly the most successful Well Intentioned Extremist in fiction. He kills three million people to achieve world peace...and, as far as the reader can tell, it works, though the last panel opens up the possibility that it may have all been for nothing.
Another example would be Rorschach, whose violent and murderous behavior towards criminals is fueled by his own twisted desires to protect the world and defend the good. However, due to mental trauma, he tends to view almost everything and everyone as bad and needing punishment, making him come off as a Sociopathic Hero.
V from V for Vendetta is the poster child of this trope. He wants to free England... by causing riots and crippling the government.
The head of said government, Adam Susan, is A Nazi by Any Other Name who may be the only thing keeping order in a nuclear wasteland.
One of The Flash's most dangerous enemies, Zoom, fits this pretty well. He just wants to make the Flash a better hero... by killing his friends, family, and lesser villains.
Sinestro falls into this, especially during his debut and the Sinestro Corps War. His planet was, by all accounts, lawless and wild, so he used his Green Lantern ring to conquer it and instill order, by brutally oppressing the entire population. When the Sinestro Corps starts up, he seeks out people who can instill great fear, including Batman (who refuses), so he can save the galaxy from itself. Again, by ruling the entire population through fear.
In the end of the Sinestro Corps War, Sinestro admits that what he really wanted was to improve the Green Lantern Corps by making them accept the use of deadly force when necessary.He achieved his ends either way.
The Red Lantern Corps (emotion: rage) fall into this as a whole, since their rage is universally driven by loss; all any of them want to do is avenge their loved ones, nomatterthecost. It doesn't help that their power is one of the two least controllable ones of the emotional spectrum and, as a result, they tend towards being The Berserker, destroying anything or anyone that they see as being in their way.
The Entity of Compassion, Proselyte, is dedicated to eradicating evil by spreading empathy and compassion across the universe. It sees nothing wrong with brainwashing people to make them feel compassion. Although the individuals it brainwashes are all borderline sociopaths, psychotic killers, and unrepentant monsters who are forced to wear the rings so they can finally understand why their past crimes were wrong. Indigo-1, a.k.a. Iroque the Child Killer, legitimately begged to have her ring returned and the Tribe restarted because she finally began to understand how terrible she'd been. Also, Proselyte doesn't brainwash every Indigo ring wielder, and they are capable of seeking out individuals who are fully capable of great compassion, not just those who lack it.
The Guardians of the Universe. They've been screwing up since the universe started, and while it's (usually) obvious that they are at least trying to do the right thing, more often than not, it just blows up in their faces.
The White Light Entity has committed a few morally ambiguous acts in order to save all life in the universe.
General Zod, long-time enemy of Superman, has been reinvented as this over the last year in the "World of New Krypton" storyline. Normally a conquering madman, he has been named military commander of New Krypton and is devoted to protecting the new planet by any means necessary, but he has been shown to be fairly honorable and decent. He cracked down on his sadistic minion Gor, promoted Superman in his place when he was incapacitated by an assassin, and came to appreciate his former enemy while still maintaining views that are much harsher than those of Superman's. If New Krypton is destroyed, all bets are off.
Actually, Zod and General Lane are only W.I.E.s at first glance (advancement of New Krypton and protection of Earth from aliens, both of which are understandable). Recent developments, however, show that they aren't this at all. Lane's actions are purely antagonistic and uncoerced for the most part. While he has a point about being prepared and protected against alien invasions, he has done all he can to provoke a war with the Kryptonians. And all of this is largely due to the subtle notion that he is disgusted that his daughter, Lois, is attracted to Superman. Zod is no better, as he sent his own spies, composed of Phantom Zone criminals and army grunts, to invade Earth and more-or-less complimented Lane's actions. The whole reason Zod's doing this? It's because he hasn't forgotten his blood-vendetta against the Son of Jor-El and his house and had his pride wounded by being beaten on Earth before.
Batman himself comes close to this from time to time, especially in the Frank Miller variations. It's implied that the reason Batman sticks so close to his code of no killing is because he's afraid that once he crossed that line, he would become this.
In the Batman: Red Rain sequels, Batman does exactly this. He drains Joker of blood and stakes him to prevent him from coming back as a vampire. He then has Alfred stake him to keep himself from coming back. It doesn't work, though, and he comes back, decapitating and draining the blood from many of his old enemies.
John Horus, from Warren Ellis's Black Summer. As many characters note, he just wants everyone to be good. It's fine that he thinks the US government has perpetrated an illegal war, and as a condoned costumed vigilante, he may be expected to act against it, but he decides the best way to deal with this is to kill the president.
Rainmaker from PS238. The namesake of the Rainmaker program, which was intended to discover the cause of superpowers by experimenting on metahumans that couldn't fight back, he was treated more as a lab rat than a child to be taught, and ran away after a lab accident gave his powers a boost. After finding out that the titular school has re-instituted the Rainmaker Program, the Rainmaker invades the school facility and disables several of the teachers and students in an attempt to 'rescue' the participants in the program. The Rainmaker program turns out to have changed a bit in 40 years and is now a volunteer school program for grooming metahumans with non-combative abilities for work in the private sector.
In Rainmaker's defense, though, he had been, ah, influenced by the head of Dr Irons, who was not acting with the best of intentions.
Also, the Headmaster of Praetorian Academy just wants to keep metahumans from evolving to the point where they're powerful enough to destroy the world.
The Deacon from Ghost Rider just wants everyone to go to Heaven and be at peace. So he kills them to expedite the process.
Enginehead is extremely simple in his "programming", with the single-minded directive to "fix" humanity by eliminating "flaws". When he sees that someone is "broken", he "fixes" them by tearing them limb from limb. His genuine inability to fully understand the ramifications of his actions causes Dr. Grass to peg him as not a superhero, but a new breed, here to save us all by scorching the earth until none are left standing.
To give an example: when he discovers his brother romancing a schoolgirl, he realizes that he's "broken" and "fixes" him by rearranging his face, tearing off his genitalia (and legs), and crudely stitching his body back together before altering his brain so he can't commit violent acts. Sam was a freak, but goddamn, overboard much? Later, when he hears of a drought in New Jersey, he fixes it up to the point that it becomes an equally debilitating water surplus.
The Squadron Supreme limited series was built on this trope, as the Squadron vows to use their super-powers to cure all of society's ills — even if it requires restricting civil rights and individual liberties to do so.
Baron Helmut Zemo falls here these days. While his original motivation was to avenge his father, his current MO is to take over the world...so he can save it.
Similarly, he leaked Bucky Barnes' identity to the press and essentially ruined his life...because he had genuine moral outrage over the fact that a former Soviet assassin was being allowed to wear the Captain America costume.
Subverted in Runaways. The members of the Pride keep talking about building a better future for their children, but it turns out that their plan is to help some ancient monsters wipe out all of humanity in exchange for granting their offspring eternal life. Plus, the original deal was that half of the Pride would get to live forever in paradise, so their motivations were purely selfish to begin with. Only one couple, the Yorkes, seem to genuinely think that they're doing the world as a whole a favor.
Stacy Yorkes: Before my dolt of a husband totaled our 4-D portico permanently, we visited thousands of possible futures, each worse than the last...The next generation deserves something new...and that's exactly what we're going to give them.
The Leader, Evil GeniusArch-Enemy of the Incredible Hulk, is most often portrayed as this. He wants to conquer the world and solve all of its problems (in some cases, he doesn't even want to conquer the world, just set up his own utopia). Depending on the writer, he may or may not want to turn everyone in the world into a gamma monster like himself and the Hulk, as well.
It's a good thing that Superman is Genre Savvy enough to be freaked out by the possibility of becoming this trope, since his power would make fulfilling any goals he may set pretty easy.
Superman: "I'm not a soldier of any kind...It's only a short step from there to calling yourself a crusader, or something equally dubious. Too many powerful people make these silly declarations...then it's all "holy war" and "sacred destiny". That's generally when the trouble starts."
On the other hand, when the Eradicator took over as Superman during The Death of Superman, he had no qualms about using deadly force and thought he was doing what Superman would do. However, he's shown to be shaken by Guy Gardner's admiration and a couple of What the Hell, Hero? speeches from Lois Lane and Steel.
And in Superman: Red Son where Superman was raised under the belief of communism, he does just this. Taking over Russia and becoming a Dictator to protect the people. He tries to do this to the whole world but is stop by Lex Luthor with a simple note that makes him realize he is no better than Braniac trying to put the world in a bottle.
Issue 20 of Justice League Generation Lost shows us why Maxwell Lord is willing to do all the horrible things he does: he sincerely believes that if he doesn't take dictatorial control of the metahuman community, the inevitable result will be the sort of spandex genocide we saw at the end of Kingdom Come.
Geoffrey St. John was recently revealed as one as well. His Face-Heel Turn and subsequent aiding of Ixis Naugus in becoming king is explained as him honestly believing that it's for the Republic of Acorn's own good. He's since seen what Naugus is capable of when Sonic and his friends can't actually stop him, and regrets what he's done. His attempt to appeal to Naugus's better judgement to make amends for what they've done didn't go so well.
Foolkiller. After all, who doesn't sympathize with a guy who kills fools? Just make sure you're not one. To give you an idea of how Ax-Crazy he is, when he fought Spider-Man, the hero started to trounce him good, and an onlooker commented that the guy was a fool for thinking he could beat Spider-Man. Apparently, the Foolkiller thought the guy had a point, and tried to turn his weapon on himself. (though, fortunately for him, Spidey stopped him and he was hauled to an asylum.) The thing is, Foolkiller is not one person; several criminals have held the identity over the years, and each one has a different definition of what a "fool" is. It's very doubtful they'd all agree with each other if they were all in one place.
The Captain America villain Flag-Smasher thinks that the only way to end humanity's problems is to dissolve all governments and unite Earth in a One World Order. Unfortunately, he chose terrorism as the way to get his views accepted, doing things like destroying national symbols, assassinating world leaders (especially symbolic leaders, like monarchs) and naturally, fighting Captain America, the living symbol of America. During his first fight, Captain America tried to talk him into becoming a hero; let the world see how his world government views inspired him to acts of heroism, much like Cap's own views did for him. He didn't listen. Even worse, he leads a whole organization of lunatics with this belief named U.L.T.M.A.T.U.M.
The Ultimate Marvel take on Nuke is this. Essentially created as the Captain America for the Vietnam War, he eventually felt his country had betrayed him and the very values it claimed to stand for, walking off into the jungles and disappearing. When he resurfaced, he was trying to create Super Serum to give a new army of super soldiers with which to tear down the irredeemably corrupt America that had arisen, and deliberately tried to break Captain America by confronting him with all of the atrocities that the USA has performed and the corrupt governors that have arisen, including Richard Nixon and his illegal campaign of carpet bombing in Cambodia and Laos and the C.I.A.'s ousting of a democratically elected president of Chile to install the corrupt regime of Augusto Pinochet.
In IDW Transformers, there are a band of aliens called the Reapers (not those Reapers), who all seek to end war in the universe by eliminating any violent races and destroying any thing worth fighting over.
Megatron. "Peace through tyranny." The words he's written imply that he's fighting to bring down the corrupt Cybertronian regime that condones abuse of second-class citizens. He claimed that he would never remove his fusion cannon until he no longer had to fight. It's difficult to figure out if he actually believes his own words or just uses them as an excuse to fight and kill.
Prowl has become one in recent storylines. Destroying the incriminating dataslug that Ironfist sacrificed himself for in Last Stand of the Wreckers for instance is a great example of how far he's wiling to go to end the war. This is greatly expanded upon in the current ongoing.
Amanda Waller, from Suicide Squad. Intends to protect the United States from harm. No matter if the US is in the right or wrong, no matter who she has to send into suicide missions, no matter what superheroes she deems a threat.
Headmaster Gentis from Darth Vader and the Ghost Prison was motivated with the desire to stop the constant warmongering of the Galactic Empire under Palpatine's command after he witnessed several dead imperials being incinerated by the minute. His method of doing so was by orchestrating a Military Coup against the Emperor with False Flag Operations, one of which also involved releasing a poisonous gas that severely wounded Palpatine; it didn't kill him thanks to his use of the Dark Side of the Force.
In H'el on Earth, all H'el wants is to ressurect his home planet, Krypton. Unfortunately, Earth has to be destroyed for him to bring back Krypton.