Akira in Ao No Fuuin becomes one as the story proceeds. His duty as the Byakko is to kill Oni, but as things happen, more and more Oni appear and he starts to go along the idea of "A dead Oni is a good Oni". While he certainly is only fulfilling his duty and Oni are presented as bloodthirsty, violent people who feast on humans, it's also portrayed as a very bad turn of his character and adds to the story's Grey and Gray Morality.
The Prince of Tennis' Rikkaidai tennis team, who will stop at nothing to win. Especially their captain, Seiichi Yukimura, after he gets better from his illness.
The religious branch of the Ancient Conspiracy "Soldats" in Noir were this way, despite the ironic creation of Soldats due to their persecution 1,000 years ago. Altena, similarly, will stop at nothing to see her ideals realized, for the sake of humanity, no matter how many must die, Les Soldats or otherwise.
Ironically, this is actually downplayed with Father Alexander Anderson. Yes, he's a bit indiscriminate in his targeting of vampires, as poor Seras has learned the hard way. Otherwise, not so much. And this is proven during Maxwell's Holy Crusade upon Protestant England; instead of backing up the genocidal Maxwell, Anderson is completely disgusted by his bloodlust and the killing of so many innocent Christians and readily assists Alucard in killing him.
As shown above, Maxwell is even more Ax-Crazy and fanatical than Anderson, which is truly amazing. Unlike his mentor, Maxwell is willing to kill millions of innocent civilians just to satisfy his own Drunk with Power ego, and finds an entire army of equally nuts clergy members to help him. It's the main reason why Anderson has to waste him.
Anderson's protégés, Heinkel and Yumie, tend to lean towards this as well. However, unlike Maxwell, both they and another large chunk of Iscariot (many of whom were also raised by the Scottish priest) are directly under Anderson's influence, so they don't take the fanaticism or blood-letting quite so far.
Yu-Gi-Oh! has Dartz and his organization, Doma, which wants to destroy the world in order to save it.
Yami Yugi was also an intense Knight Templar in the early manga, driving people insane and directly setting five people on fire in order to protect Yugi. Many of his punishments took place through penalty games, but still, many of them are Disproportionate Retribution. When Yugi becomes fully aware of his presence after Yami Yugi is prepared to kill Kaiba to win, Yami tones WAY down, only approaching his old levels in Season 4 of the anime-only Doma arc when he (temporarily) loses Yugi's soul to the Orichalcos seal he used.
Yu-Gi-Oh! 5Ds makes a full set with the Yliaster Trio, Aporia and Zone, who have come back from the future where Momentum has destroyed the world for the purpose of saving it. They have the power to erase and rewrite history, slaughtering people behind the scenes without most people being aware of what's happening. Then we have the Ark Cradle, which has a negative spin, cutting all power to Neo-Domino and coming down to wipe out not only the City, the heart of Momentum, but everything in a radius of 30 miles. Paradox himself comes from the same future in The Movie, with the same beliefs.
Death Note's main character, Light Yagami, a.k.a. "Kira", is a Knight Templar, though he's not as severe on punishment as other Death Note users. In fact, most of the interesting characters at least border on this; L is willing to torture people (albeit another Death Note user) to capture Kira, Mikami is eager to kill for Justice, Misa for love, and Light himself...This series has an extra-lubricated Slippery Slope.
The SOLOMON organization in Witch Hunter Robin has strong ties to the Roman Catholic Church, particularly the Congregation for the Doctrine of the Faith...better known by its truncated historical title of the Inquisition.
The Royal Knights organization from the various versions of Digimon are the incarnations of this trope, following anyone who possesses holy or god-like powers with a sense of unquestioning dogmatic loyalty. Usually, whoever is bossing them around goes nuts, and they end up acting as honorable villains until several of them wise up and turn "true good".
The Hypnos organization in Digimon Tamers are Knights Templar. They seek to protect the world from dangerous Digimon, but employ ludicrously indiscriminate (and almost never effective) tactics in doing so. They are horrific, genocidal, and downright brutal when it comes to actually dealing with the Digimon. Especially the ones that they catch...
The Holy Iron Chain Knights in Berserk are devoted to smiting out all traces of evil. The problem: they include "anyone not following our exact procedures for demon-smiting" under "evil". Because of a prophecy about a Hawk of Light, which they consider the newly-reincarnated Big Bad Griffith to be, and a Hawk of Darkness, which they consider Anti-Hero Guts to be (though it's actually Griffith as Femto), things go downhill in a hurry. Doubly applies to Inquisitor Mozgus, who believes in horrifically torturing people to "expiate their sins". The thing is, the Holy Iron Chain Knights are supposed to be strictly a ceremonial guard consisting of young noblemen whose parents wanted their heirs to have all the prestige of military service with none of the danger. It is their leader, Farnese, who is completely and fanatically dedicated to the cause. She gets better, thankfully.
Ironically, their target, Hao, could be considered this too. He wants to kill all normal humans in the world so that only Shamans remain, since supposedly only good people can see ghosts. He's also completely willing to kill other Shamans who get in his way.
An example of this played for humour is the comedy duo/Lovely Angels Love Pheromone in Akahori Gedou Hour Lovege. For even the slightest misdemeanor against them (such as calling Aimi flat-chested), they will destroy anything in the surrounding area with their Powered Armors. They have no Hero Insurance whatsoever and are, in fact, seen as villains by nearly everyone. Yet all the while, they claim that "Anything can be done in the name of justice!"
Trinity Blood has quite a few bloodthirsty crusaders for justice - notable among them is Brother Petros, director of the Department of Inquisition, who can favorably be described as "zealous though unsubtle" and accurately described as a bloody lunatic.
Petros is really more of a Jerk With A Heartof Gold, willing to listen to reason, and outright defies orders from his superior (who is a flatout Knight Templar) in order to rescue the pope instead of letting him get martyred.
An early episode also subverts this when Brother Tres Iqus, Gun KataBadassextraordinaire, declares his intent to kill an innocent child simply because he has been ordered to by his superiors, but runs out of bullets. Moments later, he empties his weapon into an attacker and walks away (revealing that he does not mindlessly follow orders from the "good guys"), which is saying something because Tres is an android.
Kaname Tosen from Bleach, whose devotion to justice leads him to join up with the Big Bad. Tosen believes that the perpetrators of injustices must be punished, regardless of circumstances; to paraphrase his own words, mercy and compassion are beautiful things, but they are most certainly not just. He joins Aizen to enact his justice on Soul Society's governors for failing to give capital punishment to his friend's murderer, and presumably for all the other bizarre evil things that they've done over the centuries, like manufacturing artificial souls and then arbitrarily committing genocide upon them. When he fought his former lieutenant, he noted that he doesn't actually care about the "justice" he preached as a captain - he simply wanted revenge. In a sense, he was saying that revenge was justice.
Jin Kariya in the Filler wants to destroy Soul Society because they created and then abandoned the Bount.
General Captain Yamamoto is this to some, thought it could easily be argued that he is willing to do evil or cruel acts to keep the universe in balance. Wandenreich leader Yhwach reveals that the original Gotei 13 were actually a group of bloodthirsty murderers, meaning this may well have been the case before Yamamoto's becoming The Atoner.
In One Piece, since the heroes are pirates, many of the Marine officers are Knights Templar, the most notable of whom is probably Admiral Akainu. The very first thing we see him do is blow up a civilian ship simply because they might have one of the scholars the World Government wanted to wipe out aboard. They didn't.
Some of the Marines, such as Akainu and Lucci, are downright dogmatic in their devotion to the concept of "absolute justice" and can give the impression of a massive, sprawling organization comprised almost entirely of Knights Templar. This is somewhat tempered by the presence of more reasonable characters like Smoker, Garp or Aokiji.
And now we've got a slighter version in the Fishman Society. Since the World Government have been heavily invoking Humans Are the Real Monsters on the fishmen, some of the more extreme segments are ready to wage war on the entire effing world to secure decent treatment of their kin. Suffice it to say that most of said kin realize how batshit insane a solution this is.
Sensui of YuYu Hakusho was a particularly brutal Knight Templar before the start of the series, believing that all demons were irredeemably evil and all humans were good, killing all demons indiscriminately. When he was given overwhelming proof that his convictions were wrong, he went completelyinsane and tried to overrun the world with demons, believing all humans to be corrupt.
Admiral Haruki Kusakabe from Nadesico is a particularly evil Knight Templar, especially in the movie, where he crosses the Moral Event Horizon.
"There is only one Justice, and it is obviously on my side."
He might be more of a hypocritical, propaganda-loving megalomaniac, however. His underling Genichiro Tsukiomi, on the other hand, assassinates his best friend at a peace conference for daring to negotiate with the evil Earthlings, on Kusakabe's orders. He's become The Atoner by the time of the movie, however.
Duo and Slur from the RockMan.EXE saga. Slur, in particular, is another example of a thoroughly evil Knight Templar.
SEELE in Neon Genesis Evangelion is perfectly willing to torture young children, kill everyone in NERV, followed shortly by everybody in the entire world, horribly, to unite mankind in a "perfect" state of existence to gain transcendence and evolve humanity to it's next stage. At least the Angels weren't so pretentious.
Many of the major noble characters in the Holy Britannian Empire are self-righteous. The Emperor believes that what he's planning to do is so righteous that conquering and dehumanising entire countries, which is the opposite of the ideology he claims, is justifiable, even though it's only buying him time. Schneizel, too, believes that world peace is worth murdering somewhere around 10 digits worth of people and then oppressing the remainder for. Even Mao has his Knight Templar moments, though he doesn't seem to care enough to actually be a Knight Templar.
Some fans view the Anti-Spirals as being thoroughly evil examples of the Knight Templar, due to their repeated crossings of the Moral Event Horizon. First, they turned Lordgenome to their side against his will, making him massacre his own people. Second, they turned Nia into their slave, and then tortured her, ripping her apart from the inside. Finally, the reason they tortured her? They were sick of merely oppressing Spiral races, and wanted to Kill 'em All. Oh, and in The Movie, the torture/interrogation scene? It involved Naughty Tentacles.
Lordgenome claims that he forced humanity underground and killed all who came to the surface in order to keep the Anti-Spirals away from his planet.
JoJo's Bizarre Adventure has Enrico Pucci in its sixth part. Pucci is a somewhat unusual case in that he was manipulated by a Card-Carrying Villain (Dio Brando himself, no less!), but he nonetheless believes that what he does is what God desires - for woe to be removed from humanity. By accelerating time to the point that the cosmos resets and then repeats itself, he's going to make humanity subconsciously aware of everything that will ever befall them in the future, meaning that they'll never be struck with shock, terror, etc. Instead, they should all be in a state of fatalistic, calm acceptance. The villainous part comes from his willingness to manipulate the various prisoners whom he imbues with Stands, and killing the Joestars and anyone else trying to obstruct him as barricades to God's will. In fact, one could argue that the final confrontation between him and Emporio, and Pucci's plans to make everyone aware of Fate being brought to nothing, is essentially Utopia Justifies the Means getting completely refuted as unjust and untenable.
A large amount of Gundam antagonists are this. Anavel Gato in Gundam 0083 fervently believes that Zeon is in the right, and is willing to sabotage a peace treaty between his side and The Federation. With nukes.
Villain ProtagonistFlit Asuno from Gundam AGE is especially worth mentioning with his quest of vengeance against ALL the Unknown Enemies (Vagan) in the name of the Messiah for Earth.
Thanks to going back in time several times to try to prevent Madoka from dying and becoming a witch, and watching her friends die and the destruction caused by Walpurgisnacht, Homura becomes one in order to prevent Madoka from becoming a witch.
Some of the witches are this. Elsa Maria "saves" people by absorbing them into her barrier. Kriemhild Gretchen, Madoka's witch form in the alternate timelines, wants to do the same thing to everyone in the world.
Then of course you have The Incubators of whom Kyuubi is part of. Beings who are trying to starve off the heat death of the universe by gathering the energy of despair from the girls that make a contract with them then eventually turn into witches. They honestly believe their doing good for the universe even if it comes at the cost of lives, both from the girls that turn and the human victims who're unaware of them.
Buraiden Gai: the Director of the Human Institute.
Wedding Peach: Scarlet/Salvia believed that reforming devils was stupid and kills even the harmless ones. Subverted as it's discovered that a devil killed her best friend- after she showed it mercy, which totally broke her. She mellows out though.
Ash/Angela even gets bonus points for being an utter Hypocrite, doing things themself that they see as capital offenses in humans.
Danzo from Naruto is one. While he does acknowledge that some of his actions are morally reprehensible, the lengths he is willing to go to, his conviction that only he can save the world, and the fact that he still believes his methods to be fully justified even when they cause most of the problems in the series, pushes him over the edge from Well-Intentioned Extremist into this trope.
Satyajit Shyamalan from Birdy the Mighty: Decode is this, believing that it's his duty as one of the "chosen" to use an alien super weapon to wipe out all of humanity except the "chosen" few. He never once remotely considers that he might not be doing the right thing, or even that he might not succeed, and he ultimately gets killed by that same super weapon without ever realizing his mistake.