Gordon Walker of Supernatural is a hunter who tries to kill Sam Winchester and other psychic kids because he firmly believes that they'll turn against humanity and that Sam is the Anti Christ. He considers his position unassailable enough that he won't let morality stand in the way of stopping Sam. He didn't think twice about killing his sister when she was turned into a vampire. She had to die.
Nearly all the angels qualify, considering they believe that they're following the will of God. And most don't want to let free will get in the way of that.
Dean: "Well, they are righteous, I mean, that’s kinda the problem. Of course there’s nothing more dangerous than some a-hole who thinks he’s on a holy mission.."
And since the end of season six, also Castiel—well, until he becamemuchworse...
Lucifer himself viewed humans as murderous apes who ruined planet Earth, which he referred to as God's last perfect masterpiece. His Humans Are the Real Monsters belief as well as his self-centered, self-righteous personality caused him to rebel against God.
Adam Monroe of Heroes is immortal and has lived for 400 years. This has led him to see the World as a never-ending nightmare, filled with war, famine, and global epidemics. Thus, he plans to create a perfect world by unleashing a virus that will destroy 94% of the planet, and giving those who survive a second chance. He also believes himself to be a God, and compares it to when God flooded the Earth and had Noah build an ark to start over.
Nathan Petrelli becomes one in the third season of Heroes. He starts off as one in Volume 4 too, but his Dragon, Danko, quickly usurps the position from under him. Nathan's plans involved simply rounding up all people with abilities and detaining them to protect national security, whereas Danko seems more interested in just eliminating them outright. They don't call him "The Hunter" for nothing.
The main Knight Templar from Volume 3 was Angela Petrelli.
The Knights of Byzantium in season five of Buffy the Vampire Slayer, The Initiative in season 4 and The Watcher's Council in season 3.
Willow was arguably developing into one of these with the season 6 premiere "Bargaining", where her absolute devotion to Buffy takes a dark and scary turn, as she proves willing to cross any line to bring Buffy back from the dead and considers even possibly evil means to be trivial compared to the life of her best friend, although bringing Buffy back was clearly a good end. It's not good for humanity for the only living Slayer to be one in jail. At the end of Season 6, Willow's desire to kill Warren for killing Tara is closer to this trope, in a probably justified Pay Evil unto Evil way. The worst problem was the She Who Fights Monsters effect on Willow, which caused her to go after less heinous targets in a short, temporary Face–Heel Turn.
Interestingly enough, Willow's decision to bring back Buffy was revealed to be very bad for Buffy, as Buffy ended up being pulled from Heaven and sent back to Earth, leaving her emotionally crushed and barely able to cope with her responsibilities.
Halfrek, unusually given that demons are typically Card Carrying Villains. She insists she's enacting justice, not vengeance.
Angel turns against his friends for a few months as he goes on a crusade of punishing the guilty (Wolfram & Hart), rather than helping the helpless.
Angel: "Let them fight 'the good fight'. Someone's gotta fight the war."
Kate, Gerard and Victoria Argent from Teen Wolf without question. While the family tradition may have begun as defending humans from werewolves, things have progressed to the point where intimidation, torture and murder of humans and werewolves alike is considered morally-justifiable by them. Chris seems to not want to become this, but is increasingly complicit in his family's more brutal acts.
Bonnie occasionally strays into this territory, depending on how you view her character.
Alaric is pretty much this during his blackouts.
To an extent, the Syndicate of The X-Files qualifies for this, as, over the series, it was revealed that they were collaborating with the alien Colonists in order to stall for time to prevent the coming invasion, and to work on a vaccine for the alien plague.
The Vorlons in Babylon 5 are clear examples of this trope - they seek to maintain peace and order through the manipulation of the "lesser races", often using very morally questionable methods. By this standard, the Shadows also qualify, as they truly believe that their Social Darwinist agenda of deception, violence, genocide, and Mind Rape is for the Greater Good.
"Infection", from the first season, finds the station under attack by a cyborg Templar. An ancient artifact infects a man, transforming him into a walking weapon designed to eradicate anyone not of 'pure Ikarran' stock. Unfortunately for the civilisation in question, the definition of 'pure Ikarran' was unsurprisingly set by a bunch of fanatical racial purists, rather than scientists, and, as a result, not a single member of the Ikarran species actually measured up to the programmed standards. Whoops. Straczynski has apologized for the Anvilicious nature of this.
The recurring antagonist Alfred Bester is a bit of a Knight Templar for the Psi Corps. The best example of this is the fifth-season episode "The Corps Is Mother, The Corps Is Father'', where we see how he appears to the other members of his organization.
Iris Crowe on Carnivŕlebelieves that her brother Justin has a destiny. And she'll do anything to help him achieve it. Unfortunately, he's the Antichrist - and "anything", in this case, involves arson, multiple homicide, self-mutilation, and incest. The actual Knights Templar on the show are actually just MacGuffins to distract us from the fact that Ben, the protagonist, is a fairly crappy savior. But Iris is just a chip off the old block compared to her father, Lucius Belyakov, aka Management, who's willing to orchestrate murder after murder so that Ben can realize his destiny. Ironically, this makes him the polar opposite of a Knight Templar Parent, since Ben's destiny is to kill Justin. That's good parenting.
Lord Dread of Captain Power and the Soldiers of the Future wanted to create a better world by fusing man with machine, removing the "weakness" of emotions and allowing humanity to be ruled solely by logic. Hence the "Metal Wars" and the subsequent "Project New Order", where the planet is ravaged and most of humanity annihilated, with the few that remain either loyal to Dread, in hiding, or in an organized resistance movement opposing Dread's empire.
While Lord Dread is plagued by the remnants of his humanity, and occasionally doubts the worthiness of the cause, the supercomputer Overmind is unflinching and resolute, and it can be argued that it doesn't share the same concern for humanity's ascension to perfection, being more focused on absolute domination by the machines.
The original Magna Defender was this in Power Rangers Lost Galaxy. After the death of his son at the hands of Scorpius, he was motivated only by vengeance, disregarding his former noble ideals and vowing to stop at nothing to avenge his son, absorbing Leo's brother Mike to start his crusade against the villain. At times he was so obsessed, he had no qualms about going through the Rangers or even civilians in the pursuit of his vengeance, and so was a frequent foe of the Rangers despite their common enemies. In the end, however, when he figured he would obliterate his foe in a strike that would likely have destroyed Terra Venture in the process, a vision of his son convinced him to renounce his plans, and a Heroic Sacrifice on his part saved the station and restored Mike in the process.
Near omnipresent in Alias, to the point where multiple terrorist cells successfully pose as CIA Knights Templar to recruit unsuspecting agents, and the core group of one of those cells goes on to become actual CIA Knights Templar.
Charmed was notorious for relying on this one. A few examples:
Paige Matthews' initiation as a witch was almost spoiled when the Big Bad of the time attempted to make her use her powers to tear out someone's heart. Incidentally, Paige's powers were staggeringly powerful in their possible implications - imagine calling nuclear weapons or lightning.
When the evil and good worlds started becoming TOO evil and good, respectively, the good world was marked by extremely unpleasant and draconian punishments for the slightest transgressions.
And an Elder, a being of great rationality and goodness, spends a good portion of his time trying to murder an innocent baby out of fear that the baby is a Dark Messiah, creating a Self-Fulfilling Prophecy.Lampshaded at one point by one of his friends in on the plan. He didn't last long afterwards.
Star Trek: Deep Space Nine's Section 31, a secret rogue Federation agency who assassinate foreign dignitaries, kidnap disloyal officers, and try to commit genocide against the Founders in the name of protecting the Federation.
Admiral Leyton, Sisko's old CO, attempted to overthrow the Federation President and establish a military dictatorship in order to protect the Federation from Dominion attack.
While their portrayal varies wildly in the various series, when Borg motive is ascribed, it's usually to a desire to bring order to the universe no matter what. From their point of view, they're doing the species they assimilate a favor, and genuinely believe that they are doing something beneficial for everyone they assimilate.
DCI Frank Morgan in Life On Mars is eventually revealed to be one of these. He began as a subversion of Tyrant Takes the Helm, being a more competent, enlightened, and thoughtful administrator than Gene Hunt, who he replaces. It's then revealed that he deliberately allowed a sting operation that Hunt has set up to be badly botched in order to reveal Gene Hunt's incompetence, thus allowing Morgan to take over and reform Hunt's department. That this will result in the death of everyone on Hunt's team is a sacrifice Morgan can live with.
Bounty Hunter Keisuke Nago in Kamen Rider Kiva plays this trope so damn straight that, at times, he borders on self-parody. For example, as a young adult, he led his father to commit suicide when he reported a simple accounting error to the police as evidence of corruption, and when lambasted by an understandably furious Papa, he replied, "Sin is sin". He's also a member of a Fangire-hunting organization and believes that all Fangire are monsters to be slain - including those who are happy to co-exist peacefully with humans. He does get better, though. Bonus points for his rider form, IXA, sporting a heavy Paladin/Holy Knight motif.
You run into a lot of these in series where the monsters aren't Always Chaotic Evil. In Kamen Rider Faiz, Masato Kusaka felt that every Orphenoch had to die, and more than once he's had to be pulled off of allies or poor schmoes who didn't ask to be born/sired/mad scienced into monsterdom and have no intention of helping the evil organization Take Over the World. However, he's worked with one or two before because his Devil in Plain Sight nature is an even bigger part of him than Knight Templar-dom, and he'll use anyone to get what he wants, including Orphenochs who aren't trying to kill anyone at the moment. But in the end, when more important things like keeping Takumi away from Mari are out of the way, all Orphenochs must go.
The Knights Templar in a few episodes of Andromeda are fanatically devoted to destroying the humanity-offshoot known as the "Nietzscheans". Their leader has dark-sided in her/his attempt to stay alive "for the cause".
In Battlestar Galactica, the Cylons have a paradigm shift brought on by Boomer and Caprica Six. They realize that they no longer want to destroy humanity, but rather help humanity. So, they take over New Caprica in order to rule humans and "make them better".
Laura Roslin edges towards this periodically throughout the course of the series, but is usually pulled back from the slippery slope by one of the Adamas.
Admiral Cain believes the cylons need to be wiped out and anyone who stands in her way is an enemy of the cause. To achieve this end, she murders an officer for refusing to obey a suicidal order, allowed her men to systematically torture and gang rape a captured female Cylon, and attempts to have Commander Adama murdered. Her absolute worst crime is abandoning civilian vessels she was transporting after stripping them of parts and forcing certain personnel to join her ship (leaving the rest of the civilians to die in the middle of space). When they refused, she had their families murdered.
The Outer Limits (1995) revival episode "A Stitch In Time" was a meditation on how Knights Templar come to be created and the price a person pays for being one. It's generally regarded as one of the best episodes of the series.
A few unsubs in Criminal Minds see themselves as heroic people ridding the world of evil by killing off acquitted criminals ("A Real Rain", "Reckoner"), vagrants ("Legacy"), or just general sinners ("The Big Game"/"Revelations").
In the Merlin1998 series, Queen Mab, the ruler of the Old Ways, is this. According to the novelization, King Constant was like this before Vortigern overthrew him.
The Magister from True Blood definitely qualifies for this trope, because of his Draconian belief system and almost fanatical dedication to the Vampire Council.
Agent Van Alden in Boardwalk Empire is the head of the local prohibition agents, and is completely insane. He is so committed to bringing down Nucky and the bootleggers that nothing else matters in his mind, and the ends justify the means. These means include torturing a mortally wounded man to death and drowning a fellow agent that he suspects of being The Mole. That he is right about that last point doesn't stop that act from serving as his crossing the Moral Event Horizon. That is, if he didn't cross it much earlier by reaching into a dying witness's gaping abdominal wound to extract a statement...
Detective Vic Mackey of The Shield would like to think of himself as one. He constantly commits acts of brutality, harassment, and murders a fellow cop in order to continue his work of taking down gangs. He is often able to continue this through intimidation and the fact that many of his victims include rapists, cop killers, and child molesters, people who appear worse than him at first appearance. However, Mackey's self idealization completely falls apart upon further examination, as the last season shows him for what he truly is: a violent, sociopathic bully only concerned with his own safety and greed.
President Bartlet from The West Wing has shades of this trope, though he's usually self-aware enough to catch himself before he goes too far, and when he's not, he's calmed down by Leo. Made particularly explicit in "A Proportional Response", where Leo chews out Bartlet for the latter's rants about how he wishes there was an American form of "Civis Romanus" (referring to when Rome's reputation for Disproportionate Retribution was so feared that no one in the world would dare harm a Roman citizen). Leo remarks that if Bartlet tried to take steps towards such a goal, he'd have to kill Leo first, promptly making Bartlet realize just what he had been wishing for.
The Commander Dopant, the Big Bad of the Kamen Rider Double special W Returns: Accel, kills any criminal, no matter what the crime. His first true appearance has him vaporize someone for pickpocketing, and he's seen having other pickpockets electrocuted.
Superintendent Fuller from Wild Boys is this. Determined to stamp out the bushrangers, he has no trouble in riding roughshod over the law he is supposed to uphold in order to do it. In the first episode, he stages an escape attempt to allow him to gun down three prisoners, including one that he had framed.
Grimm: The Grimms have a long history of killing any Wesen they encounter, and by any they kill really evil Wesen who kill and eat humans, as well as some peaceful Wesen who would not harm anyone. Nick is an exception of this because he's a cop, and befriends several Wesen. But the rest of his family such as his mother would kill his Wesen friends without second thought. Mommy's warmed up to them by now.
The reputation leads a lot of people to panic simply because he's a Grimm; even one fellow detective who turned out to be a wesen fully expected to never be seen again after Nick approached her to talk about a case. Also, we meet another Grimm who goes around slaughtering any wesen regardless of what they actually do, and says he once looked up to Nick until Nick proved to be 'too weak to do what needed to be done.' Of course, it turns out he's actually a self-hating wesen. We also get a description of some friendly wesen who, in this episode, needed protecting. The book written by earlier Grimms describe them as peaceful, good-natured Actual Pacifists... which made killing them easier.
House: Detective Tritter has this in spades. He's convinced that House needs to be dealt with by the police, even if it means dead patients, and has little respect for ethics or the law in conducting his investigation. Even House's suicide attempt and checking into rehab do nothing to change his mind.
Several antagonists in 24 genuinely believe they're actually doing everything they can to improve the country/world in spite of the fact they're doing so involves killing innocent people and genuinely participating in terrorism. Jack ultimately becomes one himself at the end of the series after finally losing all faith in the government for good. In one of the final episodes he ultimately admits he's no longer fighting for justice but simply brutal, bloody revenge, yet at the same time still insists that he's doing the good thing due to how FUBAR'd the world really is.
The Cybermen in Doctor Who technically count as this - they genuinely believe living humans are flawed and only want to help out by upgrading them.
The Doctor himself is often very close to becoming his trope, as evidently seen in "Waters of Mars". Thankfully he subverts it. For now.
Spartacus: Blood and Sand: Marcus Crassus spells this out in one scene, saying that both he and Spartacus are fighting for what they believe in and believe themselves to be the hero. Crassus is particularly brutal about enforcing his code of ethics. In one scene he sells a Roman woman into slavery for "aiding the enemy," knowing full well that she only made concessions to save the lives of her fellow citizens.
Smallville: Chloe Sullivan toyed with this in later seasons as she became more and more of an Anti-Hero. She's much more willing to take darker routes to solve problems than Clark is, and even Oliver (who becomes more classically heroic as the show goes) is surprised by the levels she'll go to. Both her Bad Future counterpart and her Alternate Universe counterpart show signs of this trope as well.
The Big Bad from the first season of Slasher is a Serial Killer who kills horribly people he considers "sinners". The original Executioner, from whom he takes inspiration, was also arrested for killing a couple for the same reason.