Zoophobia's Adina believes that she is purifying the world by destroying those she deems "evil", which more-than-often includes those who aren't truly evil.
As shown somewhat earlier in the strip, Miranda West of The Wotch walks full stride into Well Intentioned Extremity in a recent arc, where she punishes Ivan for being too intrusive in his desire to discover Anne's secrets, also condemns two innocents, and then refuses Ivan's plea that he has (apparently) learned his lesson, as well as refusing to help the ones who had nothing to do with her concerns, threatening him when he calls her out on it. But her status as a Well-Intentioned Extremist comes not just from her actions, but also from her attempt to justify it to her familiar (and herself).
Professor Broadshouders in Zebra Girl has made it his life's mission to rid the world of demons - and doesn't care who he has to hurt, damn, or kill to get the job done. Up to and including himself.
BaronWulfenbach, absolute ruler of Europa. He demands obedience of his subjects, kidnaps the children of notable Sparks to his floating citadel in the sky, sends criminals and troublemakers to the CastleHeterodyne to repair it, despite nobody even possibly knowing how to, and has burned entire towns down to the ground to contain unmanageable problems within. He's also absolutely fanatical about keeping the Heterodyne bloodline under control, which puts him at odds with the protagonist Agatha, herself the last known heir of the family. The thing is, he has a point. Prior to his taking control, Europa was a chaotic, feudal place of madness where most Sparks ran wildly and warred against each other with their insane creations, the worst of which included the exceptionally powerful Heterodyne family, which for at least fifteen hundred years had been, with two very notable exceptions, irredeemably evil warmongers singlehandedly capable of bringing Europa into ruin. Everything Baron Wulfenbach has done, however horrific, has been to restore peace and order to the country, and he did a damn good job of it too.Not only that, but once he freezes himself along with the entirety of Mechanicsburg in a bid to keep Agatha from reclaiming the seat of her power, Europa quickly descends once again into a terrible anarchy unmatched by any before.
Redcloak, if one reads Start Of Darkness, falls squarely into this. He wants to improve life for the goblinoid races, but attempts to do so by putting down the other humanoids via divine blackmail, instead of by actually helping the goblins improve their lot.
Even more so, Miko Miyazaki. A case study in what Lawful Good can do, when taken to its extremes. Justice untempered with Mercy, blind to the possibility that she could ever be wrong.
On the heroic side, Vaarsivuus is getting there as well in recent comics. At this rate, (s)he'll end up like Belkar...
If the Snarl breaks out, it's believed that it will not only destroy the universe, but render its victims Deader Than Dead. As such, half the gods are actually in favor of destroying the world now, so that their followers will at least get an afterlife. There are good and evil gods on both sides of the debate.
However, Faye, Dora, and Marten then quickly point out how wrong this is by asking her what she'd think if a mandid what she did to women who mistreat their boyfriends. She'd ask him out. And then she orders her Vespa-bot to shoot Dora and Faye, with the lasers set to "disfigure".
It's been stated that Roxy Lalonde from Homestuck doesn't really plan her actions often, and they tend to do more harm than good. But she usually means well and enjoys helping her friends, even though she's done things such as blowing up her best friend's computer and coercing her into revealing her feelings for Jake.
A clear example from Homestuck is Aranea, who wishes to create an alternate timeline where the Big Bad never comes to power, and then use her unique abilities to make that timeline become the main universe. Of course, in order to do so, she is willing to kill anyone that gets in the way, including those opposed to the very Big Bad she's trying to stop.
Feferi Peixes planned to reform her entire society to become more compassionate to others if and when she became empress, even though said compassion is shown to be more than a bit condescending. In an Alternate Universe, she succeeds, but creates a Crap Saccharine World that had no hope of beating Sburb.
Ian Samael from Errant Story comes from a culture where Elven oppression is common and many Elves wouldn't think twice before wiping him out. His goal to keep his people from being hunted down by Elves is fine; pity that he tries to do so by attempting to wipe out the Elves himself.
Darkbringer from Lightbringer strongly believes that the only way to fight evil is to embrace its ways, abandon all hope, and give up himself to darkness and despair. He believes that Lightbringer's actions give people false hope, so he wants to kill him.
SUEPR Team One, from City of Reality, attempts to protect Reality's Mary Sue Topia by destroying the entirety of the neighboring World of Magic, which has threatened to wreck their way of life. The protagonists are forced to try to stop them, despite nearly falling victim to the very same cynicism.
Weijuaru of Juathuur basically wants to make every juathuur a god, because that would mean absolute freedom.
The robot Blunt in Freefall. Just wants to protect humanity...and has no problems with a plan to lobotomise millions of robots to remove the chance that any of them could harm a human.
Michael Kappel in Collar 6 just wants to end the silent cold war between the world governments because their hostility is creating a shadow blight that is poisoning the world (not to mention causing a lot of collateral damage). But he thinks the only way to do it is to De-Power everyone but his loyalists and take control of the world himself.
Filth Biscuit: In the story Red Kate, the titular heroine tuns a western town upside-down in her pursuit of an egalitarian, socialist paradise.
Paranatural: One of the themes of the comic is extremists using good intentions to justify evil deeds... even if the deeds have nothing to do with their good intentions.
Spender is a lesser example of this theme. His goals are still unclear, but he discusses killing one of his coworkers to keep things hidden, and Isabel's grandfather claims that one day someone more heroic than him is going to end up killing him. Spender's boss knows he's obviously up to something, but also knows that not everything he is hiding is important. She jokes that she doesn't even know his middle name.
Boss Leader: I suspect he keeps secrets from me more out of habit at this point.
Forge is a powerful fire spirit who did many terrible things when he was younger in pursuit of the greater good. While he claims to have changed, and has come to Mayview to serve "the angel" since her moral compass is far more reliable than his own, he still hasn't learned his lesson. He scratches a near-mortal wound in the Ghost Train merely as a distraction, and then blames Spender when this action puts Spender's kids in danger.
Hijack is a spirit who can puppeteer human bodies. He takes control of Jeff partly because he needs to get inside the teacher's lounge, but also because he feels bad that Jeff was bullied and wants to give him some vengeance. Except then he attacks Max (in order to get in trouble and get sent to the teacher's lounge), despite Max having done absolutely nothing wrong. Max calls him out on this, saying he's just another bully. Isabel says something similar.
Isabel: He has fun hurting people, so his evil heart tells him it's for a good cause.
Dr. Eggman turns out to want to conquer the world largely to establish a scientific utopia and prevent any incidents like the ARK massacre from happening. Because his motives are so similar to Mysto's, the two are firm allies.
Malthus and the Light Demons want to preserve the ecosystem... by wiping out most of the world's population. (Malthus being named after Thomas Malthus isn't an accident.)
The Trophic Blenders seek to solve world hunger and eliminate violence... by making everyone photosynthetic. note Their argument boils down to "The root cause of all violence is competition over vital resources in limited supply. If all life-forms could directly harness the nigh-infinite energy of the sun to live, instead of having to consume one another, then there would be no need for anyone to harm anyone else, and violence would become obsolete and vanish." Note that taking a close look at how many plants interact with each other (which can get downright ruthless) quickly pokes holes in this reasoning. To this end, they kidnap people and forcibly breed them with Seedriansin order to generate a "master race" of plant-animal hybrids. Thankfully, their extremism is greatly toned down post-Time Skip.
The crowning example is arguably Drathilox, who hails from an unpublished Kirby fanfic. Drathilox, like the Trophic Blenders, seeks to eliminate violence. But where the Trophic Blenders see competition for food as the root of all violence, Drathilox instead blames prejudice, bigotry, and hatred. To eliminate prejudice, Drathilox seeks to transform all beings into Drathlings — essentially his mental slaves. Drathilox believes that stripping away the distinctions of race — and free will along with them — is the only way to abolish violence.
While it's not touched on much, even Bowser has elements of this, as it's implied that the Mushroom Kingdom persecuted the Koopa Kingdom long ago, up to and including murdering Bowser's first wife.
Last but certainly not least, we have Altair, a Catholic fundamentalist who seeks to cleanse the world of sin... which, to him, means slaughtering anyone who doesn't fit his definition of a Christian. He's responsible for both Mysto's Start of Darkness and Artemis's insanity, as he murdered their loved ones in cold blood. Despite his bloodlust, he genuinely believes he's following the will of Yawheh (a.k.a. God). Much like Miko Miyazaki above, even being stripped of his power and flat-out ordered to stop his asshattery by God Himself doesn't get Altair to realize he's wrong. God does eventually find a use for Altair, though, by setting up a Xanatos Gambit in tandem with Triglav in order to push Mysto towards redemption.