In Denazra, released online by Nat One Productions, the protagonists are chasing after a group of terrorists who claim to be trying to save the galaxy from swarms of self-replicating machines by making the hard decisions that everyone else is too scared to consider. This includes stealing nuclear warheads from a military convoy and assisting in the complete destruction of a populated planet. The worst part is, they may be right...
Lenny Priestly of Survival of the Fittest V3 has shown that he would do anything to get his sister off the island, including killing his classmates. May be subverted; there are some implications that he may be using her as an excuse to go on a killing spree, especially now that he's gone all Ax-Crazy and lost his Anti-Villain status...
Rachel Gettys from V4 is also one.
Aaron. Hughes. Yes, he's trying to find a way off the island. However, his methods are rather...extreme. At one point, he flat-out acknowledges to himself that he doesn't care if his allies get killed, just if the majority of the class gets off the island. That's not getting into his Manipulative Bastard tendencies, or how, previously, he had let one of his former friends be killed just so he could portray him as a martyr to the rest of his group. Or the fact that he manipulated another character into electrocuting someone to death, simply because both characters involved were "a threat".
Dr. Horrible. At least, in the beginning, if you believe him. He tries to convince himself that this is still the case during the "Slipping" song, probably unsuccessfully.
Dr. Horrible: Then I win, then I get everything I ever/All the cash, all the fame and social change/Anarchy, that I run!
His fish metaphor when he first speaks with Penny is another good example.
Dudley Griffin of KateModern is one of the few people prepared to confront the Order head on. Pity he's such a violent jerk.
The SCP Foundation, and that's putting it lightly. They capture Eldritch Abominations, Artifacts of Doom, things man was not meant to see and keep it all contained to protect humanity since many of these things could cause The End of the World as We Know It. So they use prisoners as Cannon Fodder to face a lot of the worst danger and testing, perform memory wipes, cover ups, have people killed and do horrible things to even the more benign SCPs sometimes. To make matters worse, every split off group in their universe is bad enough they are the good guys if only for comparison's sake. That it's run by a dozen people at the very top makes them especially prone to this. They also managed to aggravate some paranormal entities into being malevolent or, in a few cases, created them outright. They uphold The Masquerade pretty well, though, so most of humanity doesn't know they exist.
Dr Steel wants to make the world a better place (for himself), a "Utopian Playland", by taking it over - with giant robots if necessary - and becoming World Emperor.
Brother Joseph: Y'see, these are good people who try their best to raise their children who aren't corrupted by the lust for dominance that the outside worships. But for every group of good people, there needs to be an evil man who keeps that knowledge of how tempting it can be. And I AM that evil man.
Dr. Diabolik of the Whateley Universe. He's dedicated to making humanity better, and he's found a way to 'awaken' hundreds, if not thousands, of people at a time. It involves raiding an entire medium-sized city and doing things that unfortunately cause the deaths of maybe hundreds each time. He also turns a profit on the deal, so he can afford to keep doing it.
Lord Doom has a plan to save humanity from overpopulation, hunger, crime, war, and tyranny. His plan promotes universal literacy, tolerance for other ethnicities, political creeds, and sexual orientations, grant universal health care for all, and generally make life more pleasant for everyone, as long as you didn't mind giving up a couple of small, tiny, insignificant things in the meantime...things like a right to vote, or freedom of speech, or the right to choose your own occupation. Small things like that. Oh, and he's in charge. Forever.
Suburban Knights: Jaffers and the obstacles (except for Suede at the end of part 5) just want to protect the gauntlet from Malecite so that he cannot pose a threat to our technology-dependent world. In the process, however, they're willing to fight and kill anyone also looking for the gauntlet in order to prevent that from happening.
Atop the Fourth Wall: Lord Vyce wanted to save the multiverse from 'The Entity', so he goes around protecting other universes by conquering and enslaving them.
In The G Mod Idiot Box, DasBoSchitt's way of defending Renamon from people who portray her in a pornographic manner is to repeatedly kill her and portray her in other ways (such as attacking Duke Nukem) to make these people hate her, and, as a result, has been repeatedly viewed as a Renamon hater, or even a furry hater.
In Worm, Accord became a villain in order to implement his plan to end world hunger.
Most everyone in Worm is some stripe of this, up to an including the protagonist. The tagline is "Doing the wrong thing for the right reasons."
Cauldron is an organization that regularly performs human experimentation and brainwashing on prisoners, secretly run the Protectorate, and have accidentally spawned horrible monsters that have killed millions of people, all to save the world from Scion. It turns out that their brilliant plan was to wait for Scion to start killing people and then attack him with an army of capes, which fails so badly that the apocalypse gets worse as a result.
In NoobTenshirock, who wants to "free" players from MMORPG is somewhat of a meta-case. Due to most of the characters being gamers, he mostly comes off as an Anti-Villain. His cause however seems noble to a portion of the audience due to the existence of actual MMORPG addicts (which are spoken of in mainstream media much more frequently than casual gamers in the show's country of origin). His methods have also been shown to be treating the symptoms rather than the disease: when his regular partner in crime gets her avatar banned, he contacts her to see how she's doing and her aswer is "Oh, I'm fine. Just spending my time watching TV while waiting to have enough money to buy [another game].".
The Triarian Collective from Void Of The Stars wants to end all wars in the Universe, create a universal union and bring about a golden age of universal prosperity. How do they get there? Brainwashing, genetic manipulation, massive wars, theft, assassination, genocide and mind control. Lovely.
July of May Xnocens wants to kill princess May to prevent Idius March from massacring ogres.
Good Doctor Locklear is ALL ABOUT THIS. The song released alongside it, God Syndrome, is basically a how-to guide on invoking this trope
"Let's see if you are all just bark, no bite
"Cowards like you always turn tail and take flight
Xandra from Neopets. She sincerely believed that the extent to which the Neopians idolised and revered the faeries was bullshit because despite their immense powers, they did almost nothing in return. That being said... let's just say that crashing Faerieland into Neopia is universally considered to have been a bit extreme, as responses go.