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.
After she kills her new body to save the soul of a baby and is sent briefly to Hell, Caleb resurrects the spirit of his sister, Merlyn. Apparently, this brush with darkness changed her usually angelic personality into one that was vengeful, ruthless, and downright disturbing. Completely aside from the terrifying and/or bizarre moment when she briefly speaks with a deep, demonic voice, she declares war on Buck right in the middle of a church (a Crowning Moment of Awesome for a character who rarely gets any). And when Buck possesses Caleb and dares her to kill her own brother, she goes completely too far, deciding that since everyone in the town is either aiding Buck or looking the other way, they are all evil too...so she sends a plague to slaughter the town. And all of this while still wearing white!
Jasmine. She spends years manipulating Angel, Cordelia, and the rest of Angel Investigations so that she could be born on Earth and bring about a golden age. Of course, in the process, she killed several thousand innocents, conjured a rain of fire over LA, and unleashed Angelus once again. Not to mention that she eats people and her idea of a "golden age" is an Assimilation Plot that completely removes free will. Even so, Angel and co. are uncertain if they did a good thing or a bad thing by taking her out, especially when their arch-enemies, Wolfram & Hart, actually praise them for ending world peace.
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. Had he succeeded, he probably would have gone back into the vampire hunting business (until Buffy killed him).
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.
Angel. Everything he did as Twilight was apparently to prevent anything like the Fall of Los Angeles from ever happening again.
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.
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.
William Edgars, the chief executive of a pharmaceutical Mega Corp., is developing a virus that affects only telepaths (and is fatal to them), as well as its cure. He does this not For the Evulz, nor even out of a sense of Fantastic Racism, but because he knows a war with telepaths is inevitable and wants to give “mundanes” a fighting chance. He doesn't even like taking the steps he feels he has to take, and tries to lessen the suffering of those he's testing his drugs on as much as possible.
The Soul Hunters believe that souls perish after the death of the body, and that they perform a great service to the universe by capturing and preserving them in their soul spheres. Many other races—the Minbari especially—have a rather different opinion on the matter.
Alfred Bester wants to protect Human telepaths from persecution from the "mundanes". He doesn't care of anyone he has to kill or brainwash to do so, and he and other leaders of the Psi Corps are the reason why the war between human telepaths and mundanes is inevitable.
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.
Tom Zarek sees himself as this, in universe. It's the perspective of other characters that show he's more of an ego-centric power seeker.
BIMA Satria Garuda: The villainous organization VUDO wants to bring life to the Parallel World they hail from, which would be a good goal in itself, the problem being they want to accomplish this by the invasion of Earth.
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.
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. Notably, in a later season Buffy admits to Giles that she would have let them do it if she knew then what she knows now.
The Mayor honestly thinks life under his rule post Ascension is for the best for everyone.
Severin plans to use the Time Travel powers he got from Illyria through Mega Manning to go back in time and stop the Twilight crisis from ever happening, thus stopping the rise of zompires and the end of magic. The problem is, doing so would cause an instability in space-time that would rip reality itself apart.
During Drusilla's brief bout of sanity circa Season 9, she uses a demon to remove mental trauma from anyone who asks; the downside is that they go insane as a result.
The General thinks that the Slayer Organization really is a threat to world peace.
What Genevieve thinks she is, planning to kill a "misguided" Buffy and install Slayers as leaders of a corrupt world.
Faith loads up on weapons after learning of a Back from the Dead, supposedly reformed Angel being in possession of a magical glove, scared of who he might kill. When she finds Giles had been attacked she immediately thinks 'Angel' and defies everyone in a bid to kill him. Then there was the time she and Angel discovered demon blood that could heal and even turn vampires back into humans. Because of how obsessed he was with making amends Faith intended to force it into him, and was just about to do so when she learned it would have done a lot more harm.
Whistler's plan to restore magic, as well as the Twilight arc, would have and will kill billions, but he legitimately believes it's the only way to save the rest of the world.
The last season of Burn Notice gave us James Kendrick. Kendrick is the antithesis of My Country, Right or Wrong; in his military days he refused an order to massacre a village and slit the throats of every member of the team that carried out the order in his team's place. When Michael is sent undercover to bring him down, Kendrick's first mission is to prevent MI-6 from protecting a monster and his second is to protect a good peacemaker from being assassinated by rebels of another nation.
Gideon, the Big Bad. He believed Wyatt, born of a Charmed One and Whitelighter, was too powerful a being to remain good. He believed he needed to be stopped. Not that Wyatt at this time is only a few years old. What Gideon didn't realize, after hearing about a future where Wyatt did turn evil, was his pursuit of Wyatt for weeks in basically Hell is what caused the boy to turn evil eventually. He was willing to go so far as to work with his Evil Mirror opposite, which just unbalanced the world even more.
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.
Cold Case had the oneshot character Iris Keening in the episode "WASP." In the present she's every bit the stereotypical kind elderly lady, but in her youth she was actually a tough-as-nails commanding officer in the Women's Air Service Pilots, among the first women ever to serve in the military. When one of her subordinates, Vivian Lynn, learned that another WASP pilot had been accidentally killed in what was supposed to be a prank by a male pilot and prepared to go to the General with it, Iris murdered Vivian, knowing that all doing that would accomplish would be getting women banned from flying. Sixty years later and she still doesn't have a shred of remorse, feeling that she basically singlehandedly saved the future of women in the military.
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 Sisters of Plenitude, from "New Earth". They're curing patients of their hospital quickly and efficiently... by way of horribly infected cloned humans with every known disease in the galaxy. The episode plays with this a little, as some of the sisters callously execute the clones who began thinking and feeling, and one seems more concerned with the Sister's reputation after the clones escape, carrying disease with them.
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 but one man 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.
It could be argued that the Church in the 51st/52nd century is composed of these. Bishop Octavian would be a good example.
And by their own lights, the Silence is probably this. It's revealed they were trying to prevent another Time War happening by the Daleks returning while an army of Monsters is waiting round Trenzalore.
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."
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.
Fringe: Walternate seems to fall into this category. Yes, he wants to destroy our universe, but for all he knows there isn't any other way to save his. He thinks the two universes are at war. True, he is openly malevolent towards Olivia while she is trapped on the other side, along with anyone that helps her and is quite ruthless, but he occasionally has higher moral standards than Walter. Most obviously displayed when he flat-out rejects his top scientist's idea to text cortexiphan on children, an idea that Walter developed and executed far before the conflict between the universes began. Though it was later revealed that Walter only did that in an attempt to find a safe way to cross to the other universe and return Peter home.
Yggdrasil is seen as this post-episode 19, as they are trying to prevent the Helheim Forest from over taking the world. The following episodes go on to reveal the lengths they're willing to go to to stop this from happening (which goes up to and including the worst-case-scenario of making transformation trinkets to ensure the survival of a billion people then killing off the other six) but soon after it's revealed that no one is actually well-intentioned. A good chunk of Yggdrasil don't care about the ends (their own goals are more important) and the only one who does care is deeply upset with the means and latches onto a more optimistic option the first chance he gets... which gets him overthrown by the former.
After Yggdrasil's done and over with, along with a group of people who control Helheim Forest, a victim of their extremism steps in and declares his vow to destroy the world. When Kouta confronts him in the final battle, he points out that his experience taught him that the strong hurt the weak because they lost their compassion in the process of being strong. His conclusion? Kill all of humanity and replace it with his own kind of race, one that wouldn't trade compassion for strength. Kouta knows where he's coming from, but believes he's going about it the wrong way.
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".)
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.
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: Rebecca Winstone. 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.
Mystery Diners on the Food Network, a show that features restaurant owners or managers calling in a surveillance team to detect problems in their restaurant, occasionally has this as the issue in question, such as with a manager that used to be a drill sergeant; the problem is resolved rather easily in the end.
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...
The Empress Dowager (Lao Fo Ye) in Princess Returning Pearl basically just wants order and propriety to be kept to a strict standard in her court. She also doesn’t want her grandson to marry a girl she perceives as an uneducated nobody, even if it is true love. She is harsh to Xiao Yan Zi and Zi Wei, peaking at her Kick the Dog moment when she tortured Zi Wei to the point where she almost died, but that was because she believed Zi Wei was trying to get the emperor killed. Order Han Xiang to commit suicide was even more justified since Han Xiang did basically intentionally physically hurt the emperor, which was, by the standard of the time, a big no-no. Ultimately she has no personal malicious agenda, having already risen as far as she possibly could in the court.
Ken 'Hutch' Hutchinson in "Soul Train". 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 Dark Tower" ends with the power being turned back on, and Randall Flynn uses the opportunity to launch Intercontinental Ballistic at Philadelphia and Georgia. He declares that a new nation can only emerge from the ashes of the old, that he is a patriot, and then shoots himself in the head. It turns out that he's working for the President of the United States, who heads the American government in Guantanamo Bay, Cuba, and they intend to return to the USA and retake what's theirs.
Salem: Cotton Mather, arguably. He's brutal and overzealous in his effort to hunt down witches, but they do exist, while everything he says about them appears to be true. However, he's also being tricked by them into condemning innocents. For what it's worth, his partnership with John Alden is starting to point him in the right direction.
Cotton's father Increase is even worse. Though he has a better intuition than his son, he's also much more ruthless. His attitude seems to be "Kill everyone accused of witchcraft, and God will judge who's guilty or innocent."
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.
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.
The Borg have shades of this too. At the most basic level their intentions are good: they want to bring order to chaos and improve the quality of life of all sentient beings. How they choose to go about it, however, is by forcibly attempting to assimilate everyone they meet into their Hive Mind, which puts them in conflict with the Individualist, Freedom-loving Federation. In fact, individuality and free will seem to be completely alien concepts to them; they genuinely don't understand why someone wouldn't want to be assimilated.
Garak in Star Trek: Deep Space Nine does have standards. He is also quite utterly unapologetic about the rather horrifying things he has done (and does).
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!"