Elfen Lied: Nozomi's father only attempted to prevent her from realizing her dream of becoming a singer because she suffered a throat defect that may cause her to lose her voice, the very same kind that her mother suffered from and which eventually drove her mother to suicide. Unfortunately, his methods of preventing her involved physical abuse, which left Nozomi with self-esteem issues and a bladder control problem.
Furumori from Dragon Crisis!. He was angry at the society because, when he was a researcher there, a female researcher he was working with was afflicted with a cursed precious treasure. He wanted to get a lost precious from one of the higher ups, but they constantly refused, which caused her to die. As a result, he went rogue and kidnapped/raised a girl to help him steal lost precious in order to share it with the world. Unfortunately, he didn't care how he got it and who had to get hurt or die in the process (although, in the anime at least, they never show him or Ai, his "dog", actually killing anyone, although he does try to do that to Ryuuji).
Almost the entire cast of Code Geass. In fact, it's probably the point of the series.
Magnificent Bastard Lelouch is actually a well-intentioned extremist. His primary goal is overthrowing the oppressive Social Darwinistempire because it tramples on those who are weak or kind-hearted. Oh, and there's lots of mass murder of its third-class citizens and anyone who lives in a country that it wants to take over. In a subversion, even he has trouble stomaching some of the steps it takes to achieve his goal, as seen when he becomes physically sick after killing a half-brother who fully supported the empire - and more than that, killed several thousand people to keep his illegal experiments hidden - and nearly breaks down after unintentionally causing the death of his beloved half-sister who was much nicer and dedicated to similar but less extreme goals. In all, it was a choice between a terrible, terrible thing, and an even more terrible thing. Except for the Euphemia thing. He was willing to give up rather than oppose her. The plot would've ended right there if it wasn't for a Diabolus ex Machina in form of Lelouch's Geass suddenly activating and making Euphemia Ax-Crazy and forcing Lelouch to make the best out of a bad situation.
Then the show really messes with the audience when it reveals that both of Lelouch's parents, Emperor Charles (whom he despises) and Marianne (whom he admires) intended on creating an ideal world free of war, strife, or lies, by slaying the gods and starting their own version of Ragnarok. Oh, and they ask him to go along with it too. Though it's likely that the plan wouldn't have worked anyway, due to certain things in the first season.
Lelouch throws the "Well-Intentioned" out of Extremist when he becomes a despotic overlord and Emperor of the world, and moves to execute any and all political opponents. Oh, wait, no, that's how he wants to portray himself, so that once the world's hate is concentrated on him, he can arrange for himself to be publicly assassinated, ending the chain of hatred by setting up the infrastructures and political status quos he had set up earlier himself and achieve world peace through his death, symbolically killing the world's hatred with him. It's all but directly implied he got better after that, but never said explicitly.
Schneizel had his own designs for bringing about world peace. They just happened to involve nuking a bunch of key cities and using the Black Knights and his own sister Nunnally as pawns.
Even Nunnally, of all people, becomes one when she mixes parts of both Lelouch's and Schneizel's strategies for world peace to concoct her own, somewhat less drastic, scenario. She had indisputably good intentions, but the plan still involves threats, nukes, social engineering, and effective world-domination. It most definitely runs in the family. To her defense, she didn't plann to use nukes, but she just couldn't stop Schneizel, who had been using her. So her plan was to get along with him and, when opportunity arrived, to get rid of him and Damocles, which would become symbol of hate.
Both of them were Char Aznable from the first Mobile Suit Gundam series, or, to be more precise, Char's Counterattack, in which Char tries to make the Earth uninhabitable to force the population to migrate into space, which he believes will prevent wars by making everyone a Newtype
PLANT Chairman Gilbert Durandal in Gundam SEED Destiny, inspired by Rau Le Creuset's inability to understand his own existence (which drove him insane and allowed him to nearly wipe out the human race), decides that human conflict stems from their dissatisfaction of their own roles and abilities, and attempts to implement an utopian society through the Destiny Plan, which would craft a world civilization under genetic determinism. To this end, he is perfectly willing to manipulate the masses, assassinate his political opponents, destroy countries, and use superweapons, all while maintaining an extremely high level of charisma. Durandal also believes that uniting the world will prevent future Le Creusets from having any real success. After all, if there's only one nation, there won't be different factions for people like Rau to set against one another. To his credit, his goals also included the elimination of LOGOS, a military-industrial complex that was perpetuating War for Fun and Profit (mostly profit, since they owned most/all of the mobile suit manufacturers).
Zechs Merquise/Milliardo Peacecraft of Gundam Wing, who became convinced, in the final episodes of the anime, that the only way to end humanity's penchant for war was to destroy the Earth, the cradle of humanity's bloody history, as he believed that the people of the space colonies were purer in purpose in regard to peace than those who lived on Earth. More than that, though, it was an idea hatched by Zechs and Treize to show humanity a conflict so bloody and violent that humanity would lose the will to fight ever again. It's sort of like an intentionally planned World War I, and actually ends with the same results: mainly, that people DO lose the will to fight...for a while.
G Gundam has Master Asia, Domon Kasshu's Old Master. When he's first revealed as a villain, he seems to be just another brainwashed minion of the Devil Gundam, but he eventually reveals that he's Not Brainwashed and is aiding the Devil Gundam of his own free will. From his time on Earth in the previous Gundam Fight, Master Asia concluded that humans were destroying the planet. The Devil Gundam had been made (as the Ultimate Gundam) to restore the Earth with its nanomachines, but, due to a malfunction, it concluded that this mission required it to Kill All Humans. Master Asia agreed. When Domon finally defeats Master Asia near the end of the series, Master sees the error of his ways. But Redemption Equals Death.
Gundam 00's Celestial Being. The whole point of their actions is to beat up/kill any human factions who wish to wage war against each other. They get better about this as the story progresses, and become much more selective in their targets. They even ally with an anti-government military force in the second season. Their overall goal of eliminating conflict through force remains, though. It was all The Plan by Schenberg to unite humanity in order to prepare them against an Alien Invasion.
All Ryoko Asakura wants to do is to break the status quo and incite some reaction from the titular character. Her method happens to be trying to murder the narrator, and major love interest, Kyon. When she returns in the tenth novel as a Boxed Crook, she still wants to kill Kyon because she still believes that her actions were justified. Still, she protects him, because she wants to be the one to kill him.
Also, both Tachibana Kyouko and Fujiwara, in the Anti-SOS Brigade, qualify as well, though the latter is more of a Knight Templar. Kyouko wants to protect the universe from destruction, and so believes that Sasaki, rather than Haruhi, is the best person to have godlike powers, since Sasaki has no desire to reshape the world. She says that she has no ill will against Kyon, but disagrees with the SOS Brigade's philosophy. Fujiwara, on the other hand, believes that the existence of Stable Time Loops in this series prevent any possibility of free will, so he wants to prevent the discovery of time travel, thus changing history and proving that free will exists. Unfortunately, he will stop at nothing to achieve this goal, including the attempted murder of children.
Celestin from Ah! My GoddessThe Movie is, in tune with the emphasis on romance in the series, a much lighter version of this. Still, the fact that he purposely erases Belldandy's memory of her love for Keichi specifically, infects her with a virus that uses her as a contact point to infect Yggdrassil, and forces her to undergo a procedure that has a 16% chance of working properly, otherwise erasing all of Bell's memories of not only Keichi but her sisters and Heaven itself, all in order to gain the power necessary to eliminate sadness and suffering from the world by force shows that he's not exactly nice either.
The Anti-Spirals from Tengen Toppa Gurren Lagann are out there to prevent the universe from being destroyed by an overload of Spiral Power, and in order to do that, they take The Heartless way and prevent any feelings of hope and courage from sprouting around the Universe.
Ironically, he actually commented on this himself a while earlier:
Rossiu: Sometimes the best intentions can lead us down the wrong path.
Finally, at least from the viewpoint of the three above, Simon himself and the Dai Gurren-Dan, who are doing exactly what the antagonists fear will destroy humanity/the Earth/the universe, and with no other justification than "Who the hell do you think we are?" Some of them come around by the end, though.
Makubex of Get Backers is a great example of this trope. He's introduced as the villain of the I.L. story arc with the goal of creating an atomic bomb to use as a bargaining chip for the God of Infinity Fortress, in order to say 'stop controlling us or else'. Trying to make a deal with God by using an atomic bomb may not be the best METHOD of madness, but, at heart, his goals are to make life better for the enslaved masses of Infinity Fortress' Lower Town, which has become a living Hell since Ginji left.
In Space Runaway Ideon, the Buff Clan's supreme military leader, Doba Ajiba, was willing to risk the destruction of the majority of his race if it meant the destruction of the Ideon. When one considers that the power of the Ide was forcing the Earthlings and Buff Clan to genocidally slaughter each other, it probably is the lesser of two evils.
The home planets of both the Earthlings and the Buff Clan were just destroyed by meteors, leaving those fighting as the few left of their kind.
The villain of the third Tenchi Muyo! OVA, Z, becomes one due to unfortunate circumstances.
Nagi from Mai-Otome believes that the Otome system of sending female bodyguards off to war in place of their country's leaders is an outdated model, and wants to put an end to it (which is exactly what series protagonist Arika wants to do)...by destroying the system from which the Meisters derive their abilities, using ancient weaponry and a horde of sentient monsters (summoned by cultists willing to give up their lives for the cause).
Pain, whose goal is to eliminate war. His plan involves collecting all of the Tailed Beasts (killing their human containers in the process) to make a weapon of mass destruction that will kill millions and scare all of the countries into not fighting for a while before fighting inevitably returns, at which point one side will get hold of and use this weapon again, giving rise to another short time of "peace." Small periods of peace is his goal, which shows that he has a better grasp of human nature than Watchmen's Extremist. Human nature perhaps, but international relations? No. He fails that forever.
Danzo also qualifies. His ultimate goal, much like Naruto and Pain, is to bring about peace in the ninja world. However, he believes that this can only be done through power, to the exclusion of hindrances like emotion. He's not above brainwashing people or attempting to subjugate all other ninja villages, even if that requires the deaths of countless people, to achieve his goals. Many of the problems that are being faced, including Nagato and Kabuto going bad, are his fault. The Uchiha rebellion attempt is partially his fault as well.
Itachi is another example. He killed off his entire clan (save his brother), but it turns out he was under orders to do so because they were about to start a civil war. Had this happened, even more people would die and it could very well have led to a world war. He also joined Akatsuki, but this was simply to keep an eye on them and keep them away from Konoha as long as possible.
Tobi and Madara can also be considered this, since their ultimate goal is to end the current world and create a new one with no wars. Really, the majority of Naruto villains fall under this trope, though the lengths they're willing to go to in the name of "peace" are usually completely ridiculous.
To elaborate, chapter 678 reveals that Madara does genuinely believe himself to be the savior of mankind, and was unaware of the Jubi's Life Drinker abilities. Moments later, he's backstabbed on both figurative and literal levels by Black Zetsu.
In chapter 692, Sasuke reveals he wants to remove from the world everything that led to the just-passed crisis and start over completely, which means killing the Five Kages and controlling the Tailed Beasts.
The British Library in R.O.D the TV honestly believes that the world will be a better place if Mr. Gentleman rewrites everyone's memories and personalities however he pleases, including their own. Strangely, they never think to ask him if he thinks it's a good idea...
A Certain Magical Index: Aureolus Izzard, who isolated himself three years ago after failing to save Index from having to have her memories erased and has been desperately trying to find a cure ever since.
Several magic side characters fall under this, especially under the Roman Catholic Church, and most especially, God's Right Seat, with most of them bordering on Knight Templar.
Also Accelerator, who tried at least to make the Sisters run away by talking in an aggressive way before each "experiment" starts.
However, the "Well Intentioned" part of the trope is very suspect when it comes to anyone involved in the Level 6 development projects. Other than reaping its benefits (and likely being used again later by its supervisors), Accelerator doesn't have any good intentions in his involvement with the Sisters experiment, or with anything, for that matter, at least, until Last Order shows up.
Actually, in the case of Accelerator, this is somewhat played straight. In the spin-off A Certain Scientific Railgun, Accelerator attempts to leave the first Sister he fights injured and obviously beaten, but alive, until hes told that he is locked in the room until he finishes her off. To be fair, this is never seen in the original series.
Fiamma of the Right, who wishes to save the world through a sort of forced purification. Touma acknowledges Fiamma's basic goal as being a good one, but condemns his extremely destructive methods and his disdain for individual lives.
From the spin-off A Certain Scientific Railgun, Professor Kiyama Harumi, who developed the Level Upper as part of a scheme which ultimately led to the saving of a group of comatose children from a failed AIM diffusion experiment. What sets her apart is that, while her plan does involve putting at least ten thousand esper aspirants in comas, she prepared a cure beforehand and has the full intention of using it once she's done. She also tried more legitimate means first, but after nearly two dozen failures and the fact that the city's administration and law enforcement aren't going to budge, not least because of the whole Academy City conspiracy, she resorted to this.
In Hunter × Hunter, Meryem, the Chimeran Ant King, suddenly makes a dramatic change into becoming a Well-Intentioned Extremist from wanting to Kill All Humans. After befriending a human girl (whom he originally kept alive so he could one day defeat in the only strategy game he wasn't prodigal at), he learns that there are certain humans that deserve to live, and remakes his plan for the Chimeran Ants inheriting the Earth. Instead, he decides to protect the weak and remake the world so that it is so equal, the word "equality" doesn't even exist anymore. The extremist part? He wants to abolish the old system by force, and is only willing to protect the weak that he deems "have the right to live."
Admiral Gil Graham from Magical Girl Lyrical Nanoha A's wanted to stop the Book of Darkness and its multi-dimensional destructive ways, even if it would cost the lives of the Wolkenritter and result in Hayate being sealed away with the book.
From Magical Girl Lyrical Nanoha StrikerS, the TSAB high council, who are responsible for creating Scaglietti and letting him build combat cyborgs and artificial mages for them to ensure the safety of the TSAB controlled worlds.
Donan Cassim, the governor of the colony planet Deloya in Fang of the Sun Dougram, stages a fake coup d'état and uses it as an excuse to order a planet-wide hunt for dissidents and guerrillas, simply because he believes that the planet can only prosper as a part of the Earth Federation and that most Deloyans are opposed to independence anyway.
Elite Four Lance in Pokémon Special. He views humans as completely incompatible with Pokémon, so he plans to commit genocide against the human race so that Pokémon can live in peace and the world can return to its natural glory.
Maxie and Archie from the R/S arc had the same ambition in the manga as they did in the games. Corruption by the Red and Blue Orbs drove them Bugfuck insane before all was said and done.
There's also Mewtwo from Pokémon: The First Movie. Enraged by humanity using Pokémon as tools and disgusted by the acceptance of this by the Pokémon, he sought to remake the world by exterminating everyone and replacing them with clones. This way, he thought, Pokémon would have the freedom they deserve.
Mewtwo didn't bother asking Pokémon just why they accepted humans as masters. It may seem cheesy, but friendship and trust are what make the Pokémon world even work. Just don't expect fanfiction to acknowledge this.
Uh, dude? Mewtwo hated the fact that CLONES were being mistreated, not just Pokémon in general. In fact, the first movie (at least, the original Japanese version) states that Mewtwo wanted to wage war not only against humanity, but against ALL natural-born life in general. Contrast that with Mew, who feels that clones (including Mewtwo) are inferior and must be destroyed.
The entire cast of Mirai Nikki to varying degrees. Yes, even him. No Exceptions.
Hitomi in Code:Breaker. He just wants recognition for the scores of anonymous, mostly teenaged Code: Breakers who died in the line of duty by killing 50,000 people and the prime minister of Japan, whose estranged son is also a Code: Breaker. His goal is spat back in his face by his own protégé, who reminds him that all Code: Breakers are just superpowered murderers put to good use and that their anonymity is for the best.
From JoJo's Bizarre Adventure: Stone Ocean: the truly faithful Father Pucci, whose ultimate goal is to reach the "Heaven" he heard his mentor Dio talk about. He'll do anything and sacrifice anyone to get to it, and apparently, he does: he rewinds, remakes, and resurrects the world (that he completely messed up), but is killed before he can join it.
Funny Valentine from Steel Ball Run also qualifies; His motivation for gathering the Corpse Parts was so he could use them in conjunction with his Stand D 4 C to deflect any misfortunes that might have befallen America elsewhere, thus ensuring an everlasting golden age for his nation.
Kuze from Ghost in the Shell: Stand Alone Complex is a complete Anti-Villain and all around likable. You kind of have to cheer him on once his motives become clear and you learn more about what he has accomplished so far. But arming terrorists with guns, trying to kill the rather well-meaning prime minister with a katana, using kokaine as a weapon to damage the leadership of the countries he opposes, and building nuclear bombs to threaten his enemies puts him quite far in the deep end of extremist territory.
Gouda, who tricked Kuze into doing all these things. If Japan wasn't willing to face all it's social issues, he would force them to deal with them.
Witch Hunter Robin: the characters discover that they're a part of this when the truth about the witch-proof substance, Orbo, is revealed (it's made of witches!).
The balance of souls between worlds is so critical disruption can destroy existence itself. 200 years ago, the Quincies were so zealously trying to protect humanity from hollows that they destroyed too many souls and refused to listen to shinigami warnings. The shinigami were forced to go to the same extreme by wiping out the Quincies to save existence itself. The Ishida Quincies agree the shinigami did the right thing. The Vandenreich Quincies disagree. When they try to disrupt the balance of souls again, Mayuri is forced to kill 28,000 Rukongai subjects to correct it. Yamamoto says Soul Society would have supported Mayuri's act but he's angry that Mayuri didn't clear the bureaucratic red tape first before doing it.
The major Arc Villain of the Captain Amagai filler arc turns out to have been motivated by an attempt to correct a perceived family wrong. Captain Amagai was trying to avenge his father who had been killed by Yamamoto when he was a child. He didn't realise what his father had done, or why Yamamoto was forced to kill him, until it's too late for him to do anything other than take his own life in atonement for his mistaken vengeance.
Ichigo's inner hollow legitimately does want Ichigo to survive, but he'll go to any lengths to ensure Ichigo's survival - even if it means usurping Ichigo's body and turning him into a hollow with no moral restraints. This is why he appears whenever Ichigo is close to dying and whenever he grows stronger when Ichigo despairs — he grows stronger to eliminate the source of that despair. The "well-intentioned" part is best emphasized when the merged form of Hollow Ichigo and Zangetsu begins to cry after teaching Ichigo the Final Getsuga Tenshou, knowing that when Ichigo uses it, they will never see each other again — ultimately, the Inner Hollow has only ever wanted to protect Ichigo.
It turns out that Gin Ichimaru is this or at least, this is how he started although he deliberately cultivates the image of a Noble Demon. His motive is something the protagonists could sympathise with and support but the methods he's willing to (and does) use put him well outside the hero scale and firmly in the anti-villain scale. His methods are very extreme and drag him towards the Noble Demon he claims to be.
Old Man Zangetsu is revealed to be this in the final arc. It turns out that he's actually a personification of Ichigo's Quincy powers, taking the image of Yhwach as he appeared 1000 years prior, and had been trying to slow Ichigo's potential growth as a Soul Reaper and take his Hollow/Zanpakuto's place as his core powers. Why would he do this? To protect Ichigo from the inevitable fights and dangers he would face if he became a Soul Reaper. And for additional points, he'd originally intended to kill Ichigo if he were to become a Soul Reaper. Thank goodness he changed his mind.
Most of the villains from Getter Robo, curious for a classic Super Robot series. The Dinosaur Empire was caught up in a war of species dominance, trying to stop their extinction, while Burai and the Andromeda Flow Country were committed to stopping the use of Getter Energy - the power of evolution - before it endangered the whole universe.
Turns out, they both have very similar plans. The magical world's running out of energy, and when it goes, most of its 1.2 billion inhabitants will vanish, with 67 million being dumped onto an empty, airless Mars. Kurt wants to evacuate those 67 million before it's too late to save those that can be saved, whereas Fate realizes that it isn't fair to those that can't be evacuated, and Earth can't deal with 67 million refugees - so he'll just kidnap everyone and send them to a pocket dimension that is suspiciously afterlife-like.
The latter is kind of hilarious, when you stop to think about it. As of the most recent chapter, it seems like the Final Battle will boil down to who can save the world better.
Fate and his band also make a point of not harming anyone from Earth, except when Fate notices that Mahora will be collateral damage. But by that time, he has switched to full-on Blood Knight and no longer cares about anything else.
The eponymous Noein is suffering from grief from losing the love of his life, Haruka. He then searches for other dimensions where she might have survived, but finds that she's always destined to the same fate in every universe. His intention is then to converge all universes to stop all suffering, erase all existence and start it anew.
Yamaki in Digimon Tamers wants to destroy all Digimon, or, at the very least, every single one in the real world, good or not. He has a Heel-Face Turn when he realizes that his efforts are actually helping Digimon get into the real world by damaging the barriers.
Mirroring this, Zhuqiaomon wants to destroy all humans and conquer the real world because he feels they endanger the Digimon's chances of defeating the D-Reaper. He also does a Heel-Face Turn when Azulongmon convinces him that they should be focusing on defeating the D-Reaper instead.
X1999's Dragons of Earth seek to save the Earth from those destroying it — Humans — by eliminating them, and allowing the Earth to regrow and return to its natural state.
The three ruling students in Fly High control their school with an iron fist and won't allow anyone to start a student council because their friend, who didn't stand out physically or academically, was horribly bullied by the previous student president and stopped coming to class. At the end, they acknowledge that they've become the kind of people they wanted to stop.
Rex Godwin in Yu-Gi-Oh! 5Ds, who just wants to deal with the Signer conflict permanently by combining the powers of his brother's Signer Birthmark and his own Dark Signer Birthmark he picked up to overpower both gods and destroy the world to rebuild it anew so that the cycle doesn't start all over again in 5000 years' time.
All of Yliaster count as this, especially their mastermind, ZONE. His plan is to wipe out Neo-Domino and Momentum to prevent his Bad Future from happening again. The tool is his Arc Cradle, which he aims to use to destroy Neo-Domino and everything in the surrounding 30 miles, sacrificing millions of lives, all in a last effort to save not only billions, but the planet itself.
Yes but at the end of the Doma arc, it's revealed that Dartz was brainwashed by the Orichalcos so it wasn't exactly his fault.
Kaito from Yu-Gi-Oh! ZEXAL probably qualifies in the first season. He doesn't particularly like what he does to the people who he takes Numbers from, but he does it in order to heal his younger brother. Even Yuma respects him for this, despite the fact that Kaito never lets Yuma forget that he is on his "hit list". To make this worse, what Kaito was doing in the first season wasn't helping Haruto at all; it was a lie used by Dr. Faker, who was being manipulated by Barian in order to destroy the Astral World.
In fact, Dr. Faker himself falls into this category, but we don't find out until the end of the first season. For all his ranting like an Axe CrazyMad Scientist who wanted to Take Over the World, his true goal was simply to find a cure for Haurto. His mistake, it seemed, was trusting the Barians and letting them manipulate him, forcing him to commit horrible crimes in exchange for promises they never planned to keep.
Actually, this series is full of this Trope. Elphias is willing to commit genocide on the Barian World in order to protect the Astral World, while the Barians are willing to do the same thing to the inhabitants of the Astral World to protect their people. (Except for Vector; he clearly doesn't even have good intentions.)
Then there's Mr. Heartland, who claims he's this, even quoting the Trope Quote on the main page by Bernard of Clairvaux nearly word-for-word before his duel with Kaito in the second season; however, given his actions, it's very hard to believe he has any intentions except greed.
Jellal Fernandes of Fairy Tail wanted to create a world where everyone could be free and no one would ever suffer. He decided to do this by attempting to ressurect Black Mage Zeref, the Ultimate Evil of the entire series, and using his power to achieve that goal. Laxus Dreyar is a more minor example. He wanted to make Fairy Tail a stronger guild, but his plan for doing so was to take it over by force and boot out everyone who didn't meet his ideal of a powerful mage.
Ultear is another example, though she ironically first becomes this type of character after her Heel-Face Turn. For example, she doesn't at all have qualms with inflicting the Fairy Tail members lots of physical pain so they can awake their Second Origin and become stronger. Later, she genuinely considers killing Rogue who had done nothing wrong, because she knows that he will turn evil in the future and she wants to prevent that. However, she has a Heel Realization and doesn't do it in the end.
While not so much evil as antagonistic, Haruka of the Mai-HiME manga has the goal of having her Ori-Hime unit deal be the only one entrusted with destroying the Orphans. To accomplish this and dispose of her Orphan Resistance rivals, she tries to have Nao lure Yuuichi away by seducing him, orders Akira to steal Mikoto's Element, and kidnaps Mikoto and Kazuya. When word of this gets out, her approval rating plummets, and Mai and Natsuki defeat her and Yukino, ending her plans and resulting in the two groups working together.
Inverted with the Black Lotus Syndicate in Franken Fran. They do things like establish orphanages and give aid to the poor...in order to cause overpopulation and drive mankind to self-destruction. This ends up driving Sentinel II into becoming a straight example, burning orphanages and the like for the greater good.
Kyubey in Puella Magi Madoka Magica. What it's trying to do is avert, or at least delay, the heat death of the universe. Doing this just happens to involve turning young girls into The Heartless by driving them over the Despair Event Horizon, since those emotions can be efficiently harvested as energy for that purpose. Kyubey doesn't see anything wrong with this: its species doesn't have emotions, and so does not understand human value systems. It even thinks that it's being unnecessarily nice in the way it goes about it, since it will only make a girl into a Magical Girl if she agrees to it (though Kyubey almost never reveals all the details even after the agreement is made).
Paul von Oberstein in Legend of Galactic Heroes is a well-intentioned revolutionary with no moral borders whatsoever. He won't even blanche at such tasks as to allow the whole planet get nuked into oblivion for propaganda purposes. The most disturbing thing is that his ideas all work.
Guy from Ai no Kusabi. In order to remove the Pet Ring that binds his ex-lover Riki as a sex slave to Iason, he cuts off Riki's penis where the ring was attached. He then attempts to murder the aristocratic Iason to free Riki once and for all.
The Space Defense Force from Planetes were essentially space terrorists. They consisted of people from various nations that didn't have sufficient space-faring technology, and therefore fell behind while other nations that had a presence in space continued to get richer due to being able to exploit the resources out there such as from asteroids. Their main objective was to ensure that poorer nations got to benefit from technology and resources found in space, since many of them were suffering from civil war or lawlessness. And they tried several different methods to convince said nations to accept their demands, such as blowing up a space station or later, crashing a colony onto a moon base.
While she was never a villain, Ratchet Altair from the fifth Sakura Wars game displayed an example of this trope in The Movie. When Flower Division fighting a Brainwashed and Crazy Orihime, she was willing to kill her just so that she end this "meaningless waste of time".
Ratchet: I'm sorry, but, we must bring an end to this meaningless waste of time, Orihime.
The main villain of Tales of Vesperia: The First Strike is, believe it or not, Garista Luodur, the Imperial Knights' best strategist, who wanted to create a new type of blastia that could help the people gain full control of Aer. To do so, he created a gigantic blastia within the abandoned castle ruins and wanted to test out his own blastias. There was a negative side effect to this, though; the blastias he created and tested out produced abnormal amounts of red Aer, which turned the leaves on the trees unseasonably red and caused the resident animals and monsters of the forest to go berserk and threaten the people of different towns. None of the knights knew Garista was behind it all, of course, but Yuri and Flynn finally figured it out near the film's climax and had to attack him for the safety of the others.
Played with in Bokurano. Dung Beetle and Kokopelli enlist 15 kids to pilot a giant Robot named Zearth, which kills its pilot after a fight, just to give our universe a chance to fight for its own survival... at the expense of 15 kids, 328 trillion human lives and 32767 alternate universes! It doesn't get better by the fact that one of the originally enlisted kids wasn't even born yet!