24: Several villains, including Stephen Saunders, who threatens the US with a biological weapon to halt American globalism; President Logan in season 5, who sold nerve gas to Central Asian terrorists in order to frame them as an excuse for US intervention in Central Asia and gain oil from the area, and ordered the assassination of an ex-president to cover it up; and Tom Lennox in season 6, who seeks to inter thousands of American Muslims in the hopes of protecting the country from terrorism, and becomes involved in an assassination plot against the president when his proposals are declined. Though, in fairness, he was only pretending to go along with the assassination in order to uncover the conspirators.
From another perspective, this applies to the protagonists as well, especially Agent Jack I Did What I Had to Do Bauer. In later seasons, Jack flirts with a Heel Realization as he questions not only the efficacy and morality of his methods, but even whether his life is worth preserving.
Angel: Jasmine. Also, the other Powers in the comic series, now that they've hit upon the idea of sending angels to kill humans they think are destined to commit crimes.
Holtz as well, although with, of course, relatively smaller stakes. He was always a vampire hunter and had hunted Angel(us) long before the vampire had gained a soul. On the series, he sought revenge for Angelus' killing his family and many others he knew. While he was wrong to take revenge against a souled version of Angelus, he certainly saw himself as the good guy, and, as a vampire hunter in general, his intentions were good.
Or was he? Angel and Holtz both agree that Angel is culpable for the actions of Angelus, and Angelus' crimes would warrant the death penalty in any jurisdiction that allows it many times over. Angel believes that he can atone for Angelus' crimes in life, Holtz believes he can only do so in death.
Arrow: Season 1's Big Bad, Malcolm Merlyn/Dark Archer, decided that the only way to "save" the city was to destroy the crime-infested Glades, killing hundreds (if not more) in the belief that it will somehow improve things. Though it's entirely possible that that was just an excuse to justify his Disproportionate Retribution for the random murder of his wife in the Glades.
Babylon 5: Both the Vorlons and the Shadows are guiding the younger races to be better and stronger. If "some must be sacrificed", so be it. The fact that the two are permanently at war is the first sign that something's wrong here.
Battlestar Galactica (Reimagined): Felix Gaeta launches a mutiny because he believes that Admiral Adama is too close to the Cylons. His worldview is understandable; his actions, especially the alliance with not-so-well-intentioned extremist Tom Zarek, not so much.
Boss: Mayor Tom Kane is an example of a Subverted Trope: he likes to think that the bad things he does serve the greater good of Chicago, but he has a lot of trouble differentiating between what's best for Chicago and what's best for Tom Kane.
Buffy the Vampire Slayer: In the Buffyverse, Watchers generally tend toward this. Both Rupert Giles and Wesley Wyndam-Pryce showed themselves willing to do whatever it takes to stop a greater threat. Made more effective because, initially, they tend to come off as befuddled librarians.
When Watchers behave this way, they're almost always actually right. Had Giles not killed Ben, for instance, Glory would have been back and possibly killed the entire cast (Plot Armor would have prevented it, but the characters aren't supposed to know that they have Plot Armor).
Also the Order of Byzantium from season 5. Their main goal was to destroy the key to stop Glory from using it and destroying the universe.
The Avatars also qualify. Their intention was to create a perfect, peaceful utopia, but they were going to create it by means of basically brainwashing the entire human race to remove violent thoughts, and erasing from existence anyone who disturbed the peace.
There's also The Cleaners who were willing to go so far as erasing a baby from existence to keep magic from being exposed to the world.
Just Wyatt? They'll rewrite history if they need to in order to keep magic under wraps.
Criminal Minds: Villains tend to be insane, but several probably do fall into this category, like the one who, after growing up in a hellish foster home, thought it was better to kill children in their sleep than let them be put into the system.
The Judoon. In "Smith and Jones", they're trying to stop a sociopathic killer. They do this by transporting an entire hospital and everyone inside it to the Moon. Ultimately, they return it as planned, but it's still an incredible risk to take with the lives of probably hundreds of innocent bystanders. The episode Turn Left reveals that, if the Doctor hadn't intervened, everybody in that hospital (including Martha) would have suffocated. Similarly, the book Judgement of the Judoon opens with them forcing their way into a spaceship by driving an access tunnel through the hull, in order to ask the occupants about the Invisible Assassin. On discovering that they don't know anything, the Judoon leave...and don't think twice about retracting the access tunnel to leave a gaping hole.
Operation Golden Age in Invasion of the Dinosaurs. Desperate to save the planet, people mean to move back time and Ret Gone everyone save their chosen few.
The Doctor himself has always been this. Colin Baker, the Sixth Doctor, once said that the Doctor believes in "the rightness of things. It doesn't have to be beautiful, or happy, but right; it's got to be right. And when he sees something that isn't right, he's compelled to do something about it." Most of the time, it works out in his favor, but since the end of the Time War, he's become much more reckless, leading to several My God, What Have I Done? moments throughout the New Series.
In Remembrance of the Daleks, the difference between George Ratcliffe and Mike Smith (the two named human racist fascists in the story) is that Ratcliffe was only after power, while Mike Smith had been led astray from his youth and genuinely believed the Association was acting in Britain's best interests. With Ratcliffe's pedestal broken, he might have learned better in time had he not been electrocuted Sith-style by the Daleks' young slave.
Dollhouse: Boyd from Joss Whedon's show truly believes that extracting Echo's spinal fluid to make a vaccine against imprinting is the only way to stop the apocalypse from being total. He wants to use the technology that Topher developed, which he says cannot be unmade, to destroy civilization before anyone else does, and protect those he considers worthy.
Echo's original personality, Caroline, from "Getting Closer", is another example. In her past life, she becomes a much harder, colder person after years of hiding under the radar of the Rossum Corporation, trying to bring it to justice for its crimes and the death of her boyfriend, Leo. Dewitt says, "She's not evil. She's worse. She's an idealist."
Farscape: Scorpius will coerce, extort, torture, mind rape, murder, wage galactic war, and threaten to cause the mass extinction of the entire human race in his quest to destroy the vile Scarrans.
For that matter, the Scarran Emperor Staleek was similarly driven to safeguard and advance his people, and sought wormhole technology from Crichton for the same reason as Scorpius - to save lives in the coming conflict. He also felt that the Scarrans were viewed as brutish and ignorant by the other races, and that no-one would trust them to maintain peace or negotiate with the same civility as other races, and so brutal conquest was seen as the only way to preserve his race; when given the opportunity to talk and settle, he was able to overcome a hostile reaction, albeit with much effort.
Heroes: Mr. Linderman, who believes that killing 0.07% of the world's population to end violence and war is an "acceptable loss by anyone's count".
Linderman's goals are an homage to Watchmen, which also used this trope. Specifically, Ozymandias's plan to stop impending nuclear war by faking an alien invasion, even though the plan would wipe out half of New York City's populous.
Adam Monroe also counts, as after 400 years of seeing mankind's hatred, bigotry, ignorance, and warlike nature, he's decided that the best way to save the world is to wipe out most of humanity with a virus and start over with the "worthy" survivors. Again, a clear homage of sorts to Ras Al Ghul/Apocalypse, as, like them, Adam genuinely wants to help people, he's just become so warped and crazy due to his long life and powers that he feels that he's got the right to play god.
And, for the hat trick, "The Hunter", aka Emle Danko: a cold hearted son of a bitch who nevertheless sees himself as in the right, as he feels that the evolved humans are too dangerous to exist. And, given people like Linderman, Arthur, Adam, Sylar, Maury, Candice, Doyle, Flint, and the various others who've appeared in the show and in the graphic novels, it's easy to see how he arrived at this misguided viewpoint.
Both Angela, who started the Company to protect her people, and Nathan, who started the whole "round them up" program.
What about Samuel and Claire? Samuel wants to make The Reveal at the cost of normal human life and even at the cost of some specials in order to inspire non-specials into fear so that the special can use this intimidation to live freely in the acknowledgement of their power...While Claire makes The Reveal once Samuel's nasty ways are avoided with no consideration whatosever whether it would actually be better overall...It's an improvement so far as no more effort will be made to hide their powers. Indeed, she even acknowledges what her father said, "People won't change."
The Last Train: It's possible to include Harriet who is so obsessed with reaching Ark, where the nation's top scientists have been stored as human popsicles, that she frequently goes to unnecessary extremes such as sabotaging any attempt by the other survivors to settle down and start anew by poisoning their water supply to pushing the cart with all their gear and supplies off a cliff because it was slowing them down.
Law & Order: These characters turn up in the franchise all the time.
Level Headed: This show is an example of this trope. A little boy is so fed up by people littering at his school that he writes a report about it...before going on a murderous rampage, killing all the children and teachers, as well as a puppy that he sees taking a dump in the hallway. (It's interesting to note that this show was banned from viewing after the 2006 Cosboy Brothers school killing spree, due to a scene in the show that almost mirrored an incident from the real life spree almost word to word. A lawsuit was filed over the show for "Promoting the killing".)
LOST: The Others believe that they are the good guys, but most of their actions point to quite the contrary.
Michael: Who are you people?
"Henry Gale": We're the good guys, Michael.
Their main goal is to protect The Island at all costs. They follow Jacob, but due to limited contact with him, and Ben's tendency to do his own thing, they end up attempting to kill the survivors on several occasions when their true goal should be to keep them (the candidates at least) safe.
Medium: Allison's stalker, who thinks that her psychic powers are interfering with God's plans by saving people who are supposed to die and catching people who are supposed to be free. Allison tries to reason with him by suggesting that her powers are God's plan too, to no avail. The "Well-Intentioned" part is lessened a little when you consider how vicious he is not only towards Allison but also her children (there's also the fact that he's the Invisible Man from The League of Extraordinary Gentlemen movie). Deus ex Machina steps in after the now-dead stalker reveals that he's been interfering with her and other psychics' visions, resulting in the deaths of dozens of people whose very pissed-off spirits drag him to Hell.
Merlin: Uther actually believes that magic is evil and is destroying his kingdom.
As of the third series - Morgana and Morgause. They believe that Uther is evil and should be killed/removed from his throne due to his treatment of magic-users, something that a lot of viewers can get behind, but the way they go about it is...violent.
Missing 2012: Ashley Judd. Seriously, you don't want to mess with her. She'll literally KILL you if you prevent her from finding her son!
That's more in line with the Knight Templar Parent since W.I.E.s tend to try and see a bigger picture, but whatever.
NCIS: Had the daughter of the ambassador of a Middle Eastern country who was willing to fake her own kidnapping in order to prevent her father from signing a weapons deal with the U.S.. It initially seemed like she was also in on the terrorist plot to murder her father as well, although it was later made apparent that she neither planned nor intended it. Her professor, who she wasn't even aware was in on the plot to murder her father until after the faked kidnapping became the real deal, and her other co-conspirator who became greedy were the real culprits.
The North And The South: Virgilia Hazard is an abolitionist who can't tolerate slavery or those who condone it, but she comes off as an antagonist because her actions are so extreme that several characters question her life's decisions, wondering if she'd made them to spite others or to further her cause. For example, her family wonders if she married a black man because she was in love with him or if she did it because it wasn't socially-acceptable. Her hatred and extremism ends up getting her husband killed and dominates her life, although later in the series, she's able to control herself enough to provide fair treatment to wounded Southerners.
The Onion: Former prosecutor Shelby Cross of the Onion News Network takes the pursuit of justice to ludicrous and often criminal extremes. Her crusades include rounding up trick-or-treaters in her basement to protect them from pedophiles and encouraging viewers to throw suspected criminals into homemade "justice sheds". She also changes identities every three years to prevent them from being stolen, and considering that one of those identities was a patient in a psychiatric hospital...
Ken 'Hutch' Hutchinson. You can sympathize with his intentions to fight the militia, but not with his methods of blowing them up along with civilians who were in the wrong place at the wrong time.
In "Ghosts," it turns out that Randall lost his son in Afghanistan a year before the blackout, leading him to convince the rest of the DoD to go forth and use the Mathesons' power-suppressing invention to put an end to the war.
The Shadow Line: Has Counterpoint, a well intentioned Government Conspiracy. They're profiting from drug trafficking, but that profit is being used to fund police pensions rather than for personal gain.
Lex Luthor's main drive starts out as "protecting mankind from aliens and meteor freaks". Yes, Clark and Chloe are probably on those two hitlists respectively, and you know where he ended up.
Lana Lang around season five to seven (it is not made too clear) in her mission to get revenge on Lex. Chloe slams her for it. What the Hell, Hero? doesn't seem bad enough to cover it.
Tess Mercer wants to save the world. Unfortunately, the only way she can think to go about it is to team up with alien leader Zod, effectively betraying her entire race and throwing the world into hell. Nice.
Star Trek: It's a common Villain motive that even the heroes are not immune to, especially on Deep Space Nine, with Sisko's actions in "For the Uniform" and "In the Pale Moonlight" (the latter has Sisko stating that the anonymous quote formerly at the top of the page was something his father used to say), as well as everything Luther Sloan and Section 31 do.
Unusual in that the actions of Sisko during "In the Pale Moonlight" are likely a large part of what won the Dominion War, and the actions of Section 31 allowed it to end MUCH sooner, saving billions of lives. The episodes hit hard because, to protect the Federation and its people, they had to do things that they find abhorrent.
Lampshaded and played with in "For the Uniform" because Sisko chooses to deliberately invoke the trope in order to force Eddington, himself a Well-Intentioned Extremist, to surrender.
Supernatural: Vampire hunter Gordon Walker can be considered this: he kills monsters but generally does not care if innocents get caught in the crossfire.
Sam Winchester had a few shades of it too in seasons 3 and 4 where he was reluctantly willing to sacrifice one for the good of the many.
In season 6, the Big Bad of the season, to whom both Crowley and Eve played Disc One Final Boss, is revealed to be Castiel. To put Heaven on the right track by defeating Raphael to keep the Apocalypse from being restarted, he has decided anything is acceptable - in this case, allying with Crowley and opening Purgatory, the afterlife From Whence Monsters Come. The Winchester boys do their best to stop their Face Heel Turned ally throughout the final episodes of the season. He continues to plead for them to accept him and his choices up until he decides he doesn't care anymore and kills his angel allies, distracts his human allies by breaking Sam's mind, and betrays Crowley to take all the souls' power for himself.
Terror Alert: This British drama series takes this trope to the extreme, building the entire plot around it. The show is about a group of terrorist that only ever targets music related companies. Their attacks include flying a plane into a record producers building, killing a 20,000 or so people inside, going into a music store and massacring every single person inside, and killing multiple pop stars. At the end of the series, when the main protagonists finally manage to arrest the men involved, the reason that they give for their attacks leaves the cops speechless...
"We did it because the music industry is an evil corruptive hell hole that is destroy the public!"