In The Dilgar War Supreme Warmaster Gar'shan, the saner members of the Warmaster Council (like the protagonist Jha'dur, also known as Deathwalker), and the Dilgar emperor are trying to save the Dilgar race from the imminent explosion of their homeworld's sun. To do so they invaded the League of Non-Aligned Worlds, with the intent of conquering a paradise planet with adequate infrastructure already present for their people and the rest of the League for their advanced technology and worlds in which their population would be able to move when they'd grow too much for a single world, and intend to kill or enslave and work to death every single inhabitant of the League to make space and have the workforce they'll need for the first period. To be fair, they know exactly what they are, and their plan also includes making sure the next generation of Dilgar will be better people than themselves.
In the Bleach fanfic A Protector's Pride, Ichigo says this about Aizen. Ichigo claims that Aizen might have wanted to change Soul Society for the better, but he unfortunately picked up a God Complex. Along with his inability to talk to others as equals, this led to the monster he became.
The Shin Megami Tensei and Sono Hanabira Ni Kuchizuke Wo crossover Megami No Hanabira has Shusui Naito, the leader of the Yakuza Demon Tamers. During his battle with the girls he reveals his ultimate goal: to spread the Demon Summoning Program outside the city, to as many people as he can. When Yuuna protests that it would likely cause a societal meltdown as people abuse the Summoning Program, Naito counters that that is what he's counting on: when social order breaks down, people who have been historically oppressed will have a chance to use the Summoning Program to take revenge on their oppressors and claw their way to the top without being held back by arbitrary societal constraints. Ultimately, he dreams of an Übermensch that will prove themselves worthy of ruling the world through skill with the Summoning Program and the charisma to rally people beneath them, leading the world to a golden age. The death, destruction and mayhem that would likely ensue in the meantime means very little to him.
The Jackie Chan Adventures and W.I.T.C.H. crossover fanfic Kage (part of Project Dark Jade), has one of these, in the backstory — long ago, a disciple of Kandrakar, Althair the Mad Sage, led a crusade across the Known Worlds, killing thousands (especially children) in order to prevent Oracle N'ghala's vision of the "Incoming Darkness" from coming to pass.
Nerissa believes she is one, but thinks that the best way to a peaceful universe is through obedience to her and her alone.
Twilight Sparkle, as Kira, has set upon a quest to eliminate all crime in Equestria, by killing all criminals. And she's willing to kill innocents as well, in order to protect herself.
Fluttershy, the Second Kira, likewise believes in Kira's message, and is willing to kill anypony who speaks against her. Twilight objects to this.
L is willing to go to any lengths to stop Kira, no matter how morally objectionable.
Ace, leader of the Kira Neutrality Movement, believes that the only way to stop Kira is to remove her motivation (crime), and is thus pushing for harsher laws. That this would border on turning Equestria into a Police State and in no way prevents Kira from being a Karma Houdini are acceptable consequences to him.
An interesting case in Dungeon Keeper Ami. Both Empress Mercury and The Light qualify in different ways. Mercury wishes to return home, despite bonding to a Dungeon Heart, wich means if she succeads she will draw the Dark Gods after her. The Light knows that Mercury is an unwilling Keeper and has no intention of harming her native world, or the world she now lives in. However, they see no alternative but to oppose her as there seems to be no way to help her without also helping the Dark Gods.
Red Eye is this, and naturally fits Face–Heel Turn too. He started his own personal quest to rebuild Equestria, probably long before Littlepip even found her Cutie Mark, but became so driven to reach this huge goal that he let go of his morals. Soon, he had built up an empire upon the backs of slaves, hired merciless mercenaries to protect his assets, and forged a deal with The Goddess (which he planned to break once he worked out how to become a God himself, and kill The Goddess), who was a genocidal maniac herself. All of the things he did, no matter how horrible, were done to achieve the noble goal of rebuilding Equestria and bettering the lives of its inhabitants.
Littlepip can classify as one too, or at least she have shades of it. Scootaloo, on the other hand, is a more straight example.
Averted in Kyon Big Damn Hero. Koizumi absolutely refuses to use his new powers on unwilling subjects, seeking consent before experimenting on them, which makes it difficult for him to practice his powers.
Shepherd Of The Stars, a Mass Effect and Sword of the StarsFusion Fic, features the Liir as these. After several years of slaver raids from the Batarians, their agents come to the conclusion that peace will never be possible and that Batarian culture will always cause them to attack their neighbors. So they try to completely exterminate the Batarians to keep them from hurting anyone else. Only at the end of their attempted xenocide do the Liir realize that they've been duped by the same information control the Batarians used on their citizens and that most of the Batarians they killed were decent people.
The Order Triune in the The Dresden Files and My Little Pony: Friendship Is Magic crossover fanfic The Dresden Fillies False Masks see themselves as this. They seek to wipe out any trace of a reincarnated Evil Overlord called Obisidian. This is all well and good, until they've mistaken Harry Dresden, someone they've never even met, as this reincarnated villain. In the process of trying to kill them, they've kidnapped Twilight and Trixie, spied on many ponies, released a hydra that could have killed bystanders, and summoned He Who Walks BehindTWICE, severely injuring the princess. In their final act, before they were themselves sacrificed to summon a demon was to attack the Mane 6 and a disguised Princess Celestia to get to Dresden. When in turns out Obsidian never resurrected, Vigilant Watch, one of the surviving members of the Order Triune, is extremely remorseful for all her crimes, and is dismayed when she is let off so easily by Princess Celestia.
Novel Notion, who manipulated the Order into going after Harry, orchestrated their sacrifice, and planned to the same thing to the Mane 6 and Princess Celestia to become powerful himself, claims to be this, trying to create a society rule by ponies (specifically his own cohorts) by eliminating Princess Celestia and getting rid of the Order, and he totally unrepentant about it. While his reasoning for destroying the Order is pretty sound (it also made him what he was), and Princess Celestia admits that she is a tyrant, she also tells him that he would have killed many more ponies to cement his rule.
Alphamon in Transcendence: Digital Curse seems to truly want to protect the Digital World. However, he believes that every problem that has endangered it originated within the real world. As a result, he wants to completely sever any links the two worlds have to each other. Gennai notes that if such a thing were to actually happen it could even destroy the digital world, but it's unknown if Alphamon actually knows this fact as well. So far, none of his actions seem to have contributed much to this goal. His attempts to eliminate Agumon even seem to be just to spite humanity by stopping them from having a relationship with digimon.
Generals Berg, Kristiani and Olafsen in What About Witch Queen?. Their plan has shades of Insane Troll Logic (start war with Weselton to prevent war with Weselton), but they honestly believe that what they do is for the good of Arendelle, even if the queen clearly doesn't see it that way.
Disney in general
The Master of Worlds from Disneys War A Crossover Story, the Master of Worlds at first seems one, as he invokes the Utopia Justifies the Means trope in his justifications, claiming that merging all the Disney worlds into one, removing all the troubles caused in the past by travels unbalancing the various worlds, would be a greater good for which the death of the magical beings is a lesser, necessary evil. However, The Reveal that a much more nefarious force controls the Master of Worlds since the beginning pretty much proves that the Master of Worlds was not so "well-intentioned".
In Harry Potter fanfic Reparations, Draco works in the St Mungo's Department of Magical and Chemical Dependence (Chem Dep for short), which is basically rehab for magic folk. Most of the patients are addicted to a wizard drug called Chromia, but there's also a new drug called Chromia X, which is stronger, more addictive and thus more dangerous than regular Chromia. It turns out that the department is constantly running the risk of being shut down because the the board doesn't understand its importance, so the head of the department, Draco's boss, creates and distributes Chromia X because he figures that if the number of patients increases, the board can't justify shutting down the department.
Damballa in the Horseshoes and Hand Grenades story A Month of Sundays, transformed Shotaro, Haruto and Eiji into Creepy Dolls because he has been trying to find a way to revive his own grandson who got lost in the struggle of the War of the Stars. Unfortunately, he's forcing the transformation on them, shattering their minds in the process and he truly cannot grasp the idea of a human mind. Thankfully, Jun helps him see the light and reunites him with his grandson.
In The Shrouded Path, Vanitas, the Big Bad behind Silent Hill, is responsible for the torture (and often death) of the people who enter the town. However, he honestly thinks he is doing the universe a favour by ridding it of those people's evil.
According to the Lemony Narrator of Equestria: A History Revealed, the canon version of Discord is an example of this, at least when compared to the "ultimate evil" of Celestia. Given she says this at the end of a chapter describing all that occurred during his Age of Chaos makes such a claim very questionable, especially when Celestia's regime doesn't seem to do anything as obviously destructive as his.
In a more serious example, the former pegasus war hero Thunderhide is a clearer example of this, joining Luna's side after losing faith in the Celestia-Equestrian system, and believing that joining her in destroying it is the only way true change can occur.
Inner Demons: Scootaloo, having performed a Face–Heel Turn and joined up with Twilight (who herself had been consumed by her Queen of Darkness persona and become the Big Bad), is this mixed with The Starscream. She admits that, unlike Trixie and Sweetie Belle (who both also had Face Heel Turns around the same time she did), she's known all along what a monster Queen!Twilight is, and has only served her in order to get close enough to kill her and end her rule over Equestria. However (and this is where the Starscream angle comes in), she is clearly enjoying the pain and suffering she inflicts on the heroes, and more to the point, she has no intention of returning the throne to the Princesses — once Queen!Twilight is dead by her hoof, she intends to set herself up as the great Hero who saved the day, and then take the throne for herself.
Nightmare Night and Nyx: The conspiracy trying to eliminate Nyx are all convinced she's still evil and has brainwashed the Princesses, and thus has to be destroyed. They all have a collective My God, What Have I Done? moment when they realize how wrong they were.
Pages of Harmony also portrays Twilight as this. All she seems to want is for Harmony to reign in Equestria.... which she plans to achieve through performing torture and Mind Rape on her friends to extract their Elements, as well as anypony who gets in the way of her plans.
Rolling in Beaches: King Kenbroath and his clan honestly believe that ponies are descended from cursed dragons (it's actually the other way around) and that they must use the Rainbow Pearl to revert it. He doesn't care to ask anypony's permission first because he figures granting them all substantially longer lives and great power would be a blessing.
Sly Wits Paradise has the Unicorn chief Phantom Spell. He is an autocratic Unicorn chief stallion, is very (large emphasis on "very") strict on his orders and rules and has zero tolerance on misbehaviour and internal conflict, but he did so to keep his herd safe from the frequent dangers of the Everfree Forest where they live in (such as the Ursa Major that passed through the Unicorn territory later).
Misunderstandings: The conspiracy against Peter Collins, a human who ends up Equestria, is actually a subversion but in different ways. For many of the nobles out to get Peter, it is subverted on the "well-intentioned" part. They seek to target Peter, but only because they see him as a way to discredit Princess Twilight in the eyes of Princess Celestia and seek other personal gains, and show almost no concern for who gets hurt in the process. For Sergeant Peppermint York, it is subverted on the "extremist part". She genuinely believes Peter is a dangerous monster and in all fairness Peter did almost fatally shoot Aircolt Swift Wind but is unwilling to hurt other ponies to get to him, and finds herself more and more infuriated by the actions of the conspirators which have endangered lives than with Peter being free in general. When Peter is proven to be totally innocent of any wrongdoing, she confesses to the role she played.
Rainbow Factory: The workers want to keep Cludsdale full of Rainbows, which are an important part of their society. They do this by killing failed fliers, all of them children.
Ho-oh from Poké Wars wants Pokémon-kind to live in a utopia. He plans to achieve this utopia by engaging in a genocide against humanity. He later goes Jumping Off the Slippery Slope by doing things like ordering wanton killing of Pokémon, contrary to his ideals, utterly ruining the environment and not giving a damn about it, and generally being a filthy hypocrite.