Pixar has some examples - Pete Docter, director of Up and Monsters, Inc., even said what he thinks is a "true" villain ("I'm gonna wake up and do evil!") is an unrealistic character.
Waternoose from Monsters, Inc. is a father-like figure to Sulley and, his motto "We Scare Because We Care" is genuine, as he really does wish to maintain the Monster World through providing energy from children's screams. So, to this end, he has Randall build a horrifying machine that will suck the screams out of children and, as he says to Sulley, is willing to "kidnap a THOUSAND children before I let this company die...and silence anyone who gets in my way!"
Wall E's AUTO, the autopilot of the Axiom, refuses to let the inhabitants go back to Earth, even though this directive is more than 700 years old and plant life does exist (as shown at the end). But hey, he's a computer. He can't choose not to follow his programming. He's not so much a crazy A.I. as just following an ill-considered directive by a man seven centuries dead. Besides, realistically speaking, one healthy plant does not promise enough resources for the entire population of that huge ship. Which is another reason why Pixar decided to add that lengthy musical montage as the coda.
Charles Muntz from Up just wants to catch a bird and prove that he was right. Unfortunately, his methods (after going completely crazy) include killing everybody who shows up at his refuge and gets in his way.
Final Fantasy: The Spirits Within: General Hein just wants to kill the phantoms to save people from being killed by them. Unfortunately, his way of doing so involves killing a bunch more people instead of finding a solution to the problem from the roots, as the Heroine is trying to do, and actively tries to stop them. Yet, still, he is not an outright villain. He has a literal My God, What Have I Done? moment.
Recess: School's Out: Ex-Secretary of Education and former 3rd Street Elementary School principal Phillium Bennedict's reason for wanting to eliminate Summer Vacation and, initially, get rid of Recess, as well as to change the orbit of the moon during Lunar Perogee to essentially freeze the planet, was to increase the learning rate and test scores of the nation, as he felt that recess and summer vacation were causing them to atrophy, especially when Canada, Iceland, and Norway had higher test scores than them. Suffice to say, this extremism cost him both his job as principal and the Secretary of Education.
Strange Magic: The Bog King unlawfully holds the Sugarplum Fairy without trial, tries wiping out an entire species of plants and closes the borders to his kingdom for the admirable goal of preventing love potions from ruining more lives.
Zootopia: Mayor Lionheart is revealed as the one responsible for organizing the kidnapping of the missing mammals. However, he was doing so because they were going savage, and he was trying to avoid loss of life, a mass panic, and find a cure. At the end of the movie, he admits what he did was wrong saying it was "doing the wrong thing for the right reason".
Films — Live-Action
2001: A Space Odyssey: HAL 9000 is only devoted to the mission at hand, and believes that Dave and Frank will jeopardize the mission by disconnecting HAL after lip-reading from them that they intend to do so if the AE-35 component does not fail as HAL has predicted. It turns out this was due to a Logic Bomb: he had been told to lie about the nature of the mission, which conflicted with his programming of providing clear and accessible information, which triggered his breakdown.
The Amazing Spider-Man: Dr. Connors longs to create a world in which everyone is equal, a world in which illness and weakness don't exist. Injected with the Lizard serum, he comes to the conclusion his vision can be made reality by making everyone like him, even if that means forcing the change upon everyone against their will.
Thor: Loki's actions are ultimately for the good of Asgard, but he goes just a bit too far. Everything he does from the middle of the movie on are to show that he's worthy of his father's trust and every bit the equal of Thor. Granted that it overlaps with being a little Ax-Crazy, because his plan for doing this involves genocide. (Of enemies, but still.) And he goes even further in The Avengers. He thinks the humans must be enslaved in order to bring peace to them, and he doesn't mind to build his empire on thousands of corpses.
The Avengers: The World Security Council, Nick Fury's bosses. When the alien invasion begins in Manhattan, the WSC intend to nuke Manhattan to stop the invasion, killing the Avengers and millions of civilians to protect mankind.
Captain America: The Winter Soldier: Captain America initially perceives S.H.I.E.L.D. as this with regards to Project Insight, seeing the ability to launch preemptive strikes across the globe at any time as putting the punishment before the crime. it as overreaching in the name of peace and security. His concern is justified, as it's HYDRA's plan to take over. Zola and Pierce try to sell the new HYDRA as this, being severed from its original Nazi roots and essentially having the same values as S.H.I.E.L.D., but being willing to go one step further to ensure peace and order. It's severely undermined by the fact their primary targets were threats to their own political power (even the current president of the United States), and not (as Pierce tries to claim) people who were mathematically likely to become the next Bin Laden or even the next Julian Assange or Bernie Madoff. And a shot during the targeting sequence reveals they're targeting families with giant cannons that will no doubt cause collateral damage.
Avengers: Age of Ultron: Ultron wants humanity to evolve so that it'll cut all that "war" stuff out and unite to fend off the new threats coming from space - unfortunately, that means throwing apocalypses at them to toughen them up (and killing the Avengers, who he perceives as useless and who'd probably disapprove). At least, that's his goal initially. Once the heroes steal his Magnum Opus body - the Vision - from him, he's angry enough to drop that and try a different plan.
Kingsman: The Secret Service: The Big Bad concludes that existing efforts to fix global warming are hopeless, so he decides a simpler solution is to brainwash everyone to kill each other and "cull" the global population to a more manageable number.
Batman & Robin: Poison Ivy, though she does make her extremist ways known from the outset, as well as the version of the character from Batman: The Animated Series. In fact, most of the animated Bat-villains are sympathetic in their first appearance, then less so as their motivation shifts to "revenge on Batman". A similar thing happened with the version from The Batman, who was set up as even more sympathetic due to being a teenager, but, in subsequent appearances, becomes simply a villain. Subverted in the show's spin-off comic "The Batman Strikes", in which her sympathetic aspects and good intentions are retained.
In Big Game, the vice president, Hazar and Herbert. They believe that they act for the good of their country, even if it means taking down the US president and torturing him to death to create a martyr.
Blood Of The Vampire: Dr. Callistratus may be a Mad Scientist who performs human experimentations among other horrific acts, but he does what he does in the name of science, and to that end he's trying to make advancements in blood transfusions that in 1880 hadn't yet been discovered, including the sorting of blood groups. It's for this reason that he was executed for being a vampire at the start of the film: the accusations came because he was trying to transfuse blood.
The brothers' crusade against evil through vigilantism.
Category 6: when Mega Corp. Lexer ignores Dan London's repeated warnings that their power grids are woefully underprotected, he tries to make an example by covertly hacking their mainframe. Unfortunately, a freak chain of events causes this simple What the Hell, Hero? to cause the city's entire power supply to be cut off.
Batman Begins: A pretty interesting example, as Ducard and Ra's al Ghul or rather Ra's al Ghul and Ra's al Ghul's decoy believe that Gotham is a city plagued by too many evils and is filled with suffering and injustices. They also believe that murdering violent criminals is justifiable but Bruce believes that murdering a villain would be stooping to their level.
The Dark Knight Rises: Bane is supposedly continuing Ducard and Ra's al Ghul's plan, while also showing the problems with Gotham's authorities. Though the woman behind the man, Talia al Ghul, is also doing it for revenge on both her hard life and Batman killing her father.
Death Warrant: The mastermind behind the plot, State Attorney Tom Vogler, killed violent prisoners (whom he claims no one will miss anyway) because of the desperate shortage of organ transplants on the market. He also did it to save his beloved wife.
Death Wish is one of the Most Triumphant Examples of this trope, with Charles Bronson killing any thugs who menace others... granted, they have a terminal case of Too Dumb to Live going after Bronson, but still.
Demolition Man: Dr. Raymond Cocteau is an even handed example. On one hand, he did do a stand up job of cleaning up Los Angeles, ridding it of crime and disorder. On the other hand, it came at the cost of suppressing both artistic freedom and even basic human urges like sex and swearing. And when Edgar Friendly's anarchist movement got too disruptive (i.e. petty theft of food), he unleashed a dangerous criminal on the populace, causing the death of countless people. That same criminal eventually kills him for his own agenda.
The Dirties: After his and Owen's film for high school about killing their bullies, the Dirties, backfires, Matt decides to shoot a film where both him and Owen kill them for real.
Equilibrium: Father maintains a forced regimen of the anti-emotion drug Prozium on the populace, ostensibly to avoid future global conflicts like the one that drove them into semi-seclusion. Mildly subverted in the end when Father DuPont, lamenting the imminent downfall of his society, admits to Preston that he (Father) does not take Prozium, and thereby is a hypocrite.
Felon: John Smith, the "veterano" character. He took revenge on the guys who raped and killed his family, but first he wiped out their families to "purify the madness" and to show them what the loss feels like. He then became a Death Seeker to end the cycle.
Wade Porter: [on the intruder he chased and killed]: "...Shoulda stayed inside, let him go."
Godzilla and Mothra: The Battle for Earth: Battra (Mothra's Evil Twin of sorts). On the one hand, he's just doing what he was created to do (IE: Maintain balance between man and nature), but he thinks that the only way to keep nature safe is to utterly destroy humanity.
Hot Fuzz: The Neighborhood Watch Alliance of Sandford have been killing off anyone who may lower their chances at getting the "Best Neighborhood" award. Not well-intentioned enough? It's because one of the protagonists' mother committed suicide after the neighborhood didn't win once. One of the villains is the mother's husband and, thereby, said protagonist's father. He always knew that he's his father though, so this is not an example of I Am Your Father.
"If mum could see what you've become, she'd kill herself again!"
Jurassic World: Dr. Henry Wu wanted to make a scientific breakthrough by creating the Indominus rex. However, his plan also involved working with the evil Vic Hoskins to make sure that the project goes through.
Law Abiding Citizen: Gerard Butler's character in the drama/thriller is a textbook example of this. He's a man who saw his wife and daughter murdered by thugs and then watched one of the thugs get off lightly due to a dubious plea deal. This gives him a right to be pissed. And if he had simply botched the execution of one to result in a very painful death and murdered the other, he might manage to be simply an Anti-Hero and still remain sympathetic. On the other hand, murdering every single person connected to the trial in some way with an extraordinarily executed Batman Gambit, and threatening and targeting even their families may be seen as going a little too far.
The Lone Ranger: Latham Cole seems to genuinely believe he's doing the right thing with his actions. Cavendish? Not so much.
Man of Steel: General Zod's coup de etat was provoked by desperation, as he genuinely wanted to remove the ruling council who foolishly mined Krypton's core for energy causing the seismic calamity that ultimately led to Krypton's destruction. He expressed remorse but desperation with his mentor Jor-El. His attempted genocide and terraforming of Earth into Krypton again wasn't inspired by malice towards the humans but a desperate attempt to save the Kryptonian race, as he was bred as a warrior to protect his race.
Zod: No matter how violent, how cruel, every action I take is for the greater good of my people.
In Murder at 1600, it turns out the reason behind the entire murder plot was National Security Advisor Alvin Jordan wanted to force the President to resign because he felt the President was too weak in not going to war with North Korea over a hostage situation and that war was the only way to protect the nation.
Joran: I think President Teddy Roosevelt said it best: "If I must choose between righteousness and peace, I choose righteousness."
Our Man Flint. The leaders of the Galaxy organization threaten to destroy civilization with their Weather-Control Machine unless the nations of the world disarm. They promise to make the world a paradise if they are obeyed.
The Rock: Brigadier General Francis X. Hummel just wants to get pensions for the widows of soldiers who died on black operations. He's willing to take hostages and threaten to bomb San Francisco with VX gas to do it.
Saw movies: Jigsaw claims that his sadistic deathtraps give people an opportunity to truly appreciate what they have by making them fight for it. That the survivors are left emotionally traumatized and usually horrifically mutilated seems to be merely an unfortunate side effect.
Scanners II: The New Order: Dirty Cop Commander Forrester seems to sincerely believe that he's saving society by creating a police state to 'cure' crime, as the city is plagued by violent armed robbers, child killers and drug lawyers. His means of doing this is to keep everyone in line with an army of psychics.
Serenity: The Operative is very extremist but still fits in this category. He attempts to paint himself as Necessarily Evil, however.
The Secret of Kells has Abbot Cellach. He acts like a total Jerkass and is completely obsessed with building his wall, to the point where he disdains and eventually forbids his monks from doing anything else. However, the point of the wall is to keep out the Vikings, who already killed all the family he had except for his young, impressionable nephew, who now wants to do non-wall related things like go outside and create beautiful holy books. He doesn't listen when Aidan tells him that his wall won't hold and they should all flee instead, which leads to the deaths of many, many innocent people.
Skyfall: Raoul Silva, according to M. He initially went rogue not because he betrayed Britain or the MI6, but by executing unauthorised missions against the Chinese.
Stonehearst Asylum: Lamb, who only wants the patients treated humanely, but is willing to imprison, kill or torture anyone who gets in his way.
The Star Chamber: Judge Hardin is frustrated by having to let obviously guilty murderers Off on a Technicality, and understandably wants them brought to justice. He's inducted into a group of his fellow judges who feel likewise. Their method for doing this, however, involves secretly reviewing the evidence against these accused murderers, voting on whether they're guilty (it's always "yes") and sentencing them to death-via hitman. Still perhaps somewhat excusable, up to the point when it turns out some of the accused murderers aren't, in fact, guilty-and the rest refuse to even try to stop it when Harden says they have to, citing self-interest (they don't have direct contact with the hitman to protect themselves) and the rationalization that they must have done something meriting death. Cue Harden racing against time to save them from said hitman.
Star Trek Into Darkness: Admiral Marcus figured that the exploration-focused Starfleet would not be able to win a war against the Klingons, a war he thought was inevitable. He was only doing what he thought was necessary to ensure humanity's survival. The guy just ends up tapping the Moral Event Horizon when he opts to try and murder Kirk and the entire crew merely for having Khan in their custody, along with other acts.
Most members of the Galactic Empire generally believe that they are the good guys fighting rebel "Terrorists".
Count Dooku...for a while, anyway. Word of God (from Lucas and Christopher Lee himself) says that Dooku never quite realized how evil he had become, and, right to the very end, honestly believed that he was doing the right thing. The Expanded Universe has different interpretations of his motivation, though, and the novelization of Revenge of the Sith turns him into a power-hungry racist; this is especially strange because no other source depicts him that way.
Super Mario Bros.: King Koopa, although truly a Bad Boss and a self-confessed "evil egg-sucking son of a snake" dictator who often subjected criminals to De-evolution, had a reasonable motive between wanting to create a Merged Reality between his world and ours by trying to conquer the regular dimension specifically for his species' survival; it's really hard to blame him when his current dimension including Dinohattan is a Crapsack World that lacks various resources like food and water. It also, in a way, humanizes him to a point where he even says he's doing this for the future of his species compared to his second in command, Lena, who really simply wanted to simply rule everything, not caring whether her race benefited or not.
Street Fighter: M. Bison from the 1994 film is a megalomaniacal madman, but he genuinely seems to be thinking that he's performing his Evil Plan for the good of mankind. As he explains in a visionary speech, he wants to create an army of genetic Super Soldiers swearing absolute obedience to him. Then by conquering the world he can do away with conflicts based on race, nation, or creed, and everyone can live peacefully under his dominion.
Swordfish: Gabriel Sheer claims to be a necessary instrument to fight terrorists and has no qualms about going after civilians to achieve his goals.
Thirteen Days: The Joint Chiefs of Staff want to protect the United States just as much as Kennedy, but they believe it can only be achieved through war against Cuba and if necessary the Soviet Union, despite the danger that this may result in a nuclear exchange. They try to manipulate Kennedy into a situation where their men will be forced to start shooting. Discussed between Kennedy and Kenny, the latter of whom acknowledges that the Generals' intentions are understandable even if their behavior is extreme, and it may in fact end up having been the right call to make.
Training Day: Some of Alonzo's actions can be interpreted this way. Others, not so much.
Transcendence: Bree and the rest of RIFT are convinced that artificial intelligence will mean the end of humanity, and orchestrate a country-wide attack on labs doing such research in the opening. Later on, Will honestly believes he can help improve humanity, but isn't really asking permission to do it.
The Truman Show: Christof sees the real world as a place of pain and misery, so he traps his adopted son Truman in a fake world where everyone he knows is an actor, so that he won't have to face reality.
The Warlords: Jet Li's character started out as a straight hero until the half way mark, when he had to decide how to provision his limited supply of food. He had enough to feed his army for 10 days, but if he shared it with the army that had just surrendered to him, there wouldn't have been enough food for anyone to live. His solution: massacre the enemy army. He remained well intentioned and acted in the interests of the greater good, but his methods remained unsavory.
White House Down: Walker, Speaker of the House wants to nuke the Middle East with the nuclear football and ultimately end the war, but his methods are too extreme. The reason was because his son was killed in a botched CIA attempt, so he caused the events of the movie.
The World's End: The Network just want humanity to reach its full potential. They only want to kill as many as they have to in order to ensure that... Unfortunately, it turns out to still be an awful lot of killing, because humanity doesn't like being told what to do.
Magneto has always been the archetypal example in comics and the films faithfully live up to that. His plan in X-Men, is actually rather benevolent and would finally end the division between Mutants and the rest of Mankind, while sacrificing only Rogue to make it work. It's a good plan, it's just a shame his machine doesn't work! Still, Xavier desiring to stop him is apt for someone with his point of view (that is the world is fine as it is, it's everyone living in it that needs to learn how to get along with things as they are and accept everyone for their differences).
Mystique, along with Magneto.
William Stryker. At least he tries to present himself as this, but mostly comes off as Fantastic Racism.
In X-Men, Senator Kelly’s desire to introduce a Mutant Registration Act is born out of fear for others, and such fear isn't entirely unfounded.
Both Warren Worthington II and Dr. Kavita Rao, who just want to help people who society views badly.
Psylocke, Kid Omega and Callisto. Like the other Omegas, who want mutant rights but have crossed the line into mutant superiority.
Shingen Yashida from The Wolverine. In his eyes, at least, he's just trying to save the Yashida Clan from being disgraced at the hands of his "weak" daughter.
In X-Men: Days of Future Past, Magneto, Mystique, and Trask all want to do what's best for their people. All three of them are willing to go to any lengths to accomplish this. Trask is an interesting case in that he is not motivated by the typical villain desires of money or power, but he genuinely believes that fighting the mutants will unify humanity and end such conflicts as the Cold War.