The Hunchback of Notre Dame: Judge Claude Frollo wants to destroy the race of gypsies for "inflaming the people's lowest instincts". His fanaticism is bad enough at first when he kills a gypsy woman for hiding "stolen goods" (which turn out not to be stolen goods at all, but instead, her deformed baby), but add some Perverse Sexual Lust for another gypsy woman and things reeeeeally go downhill. If anything, Frollo is a deconstruction of a Knight Templar. As a Knight Templar, Frollo believes that All Crimes Are Equal, and that the punishment for every single one is death. While the gypsies have committed crimes, they have not done anything to bring this kind of punishment down on them. Frollo even has a family's house set on fire with them in it, even though they do not even know about the gypsies. This causes Phoebus to turn against him, and Frollo to try to kill him in return. He considers the gypsies to be vermin and advocates genocide against them. Frollo demonstrates why a Knight Templar, logically and realistically, would be a horrible person.
Films — Live-Action
In the 1983 Italian schlock Post-Apocalyptic film Warriors of the Wastelands, the main villains call themselves Templars, and are dead set on destroying all literature (since they feel that books led to World War III) and anyone who isn't them.
In Frailty, Matthew McConaughey's family is commanded by God to destroy demons. One of the kids sees "destroy demons" to mean "kill people". The dramatic irony is that all the people killed are murderers or worse, and the demons are real.
In a way, some of the Alliance can be seen as Knights Templar, considering that they killed thirty million people on Miranda while testing a peace-inducing chemical inhalant and the entire justification for them cutting River's brain up was to "make a better world".
The Jigsaw serial killer in Saw does not consider himself a killer. Oh, sure, he acknowledges that his actions frequently lead to horrible death, but he never pulls the trigger. And he firmly believes that the people who survive his themed deathtraps will overcome their sins and become better (though this never actually works).
The government of Libria in Equilibrium suppressed human emotion, as it was believed responsible for causing the human tendency for violence that brought about the war that practically destroyed the world, which meant destroying art, movies, and other things inductive of emotion (including cute little dogs) and terminating "sense offenders" who go without the government mandated drug called Prozium.
Jonathan Doe from Se7en believes that he is punishing the wicked by killing people that go against his belief system. It could be argued, however, that he is simply a sadistic psychopath.
The Paladins in Jumper, led by Samuel L. Jackson. They believe that they are doing God's will by murdering all of the jumpers, as "only God should have that power".
Subverted in The Wicker Man, where Sgt. Howie is introduced as a religiously intolerant, uptight Jerk Ass. However, his faith and sense of duty are presented in a more and more admirable light as the film progresses, and he's far less infuriatingly fanatical than the townsfolk.
The Christians in Agora. Special mention must go to Ammonius, who is this Up to Eleven and to the point of Stupid Evil. The pagans aren't much better, though, doing a Too Dumb to Live move, attempting to avenge "an insult to the gods".
The anonymous sniper from Phone Booth is another. His targets are usually unrepentant criminals like murderers, child molesters, and, at one point, a businessman who made off with a collapsed company's profits, leaving his employees and investors to rot. His target in the film, however, isn't any type of criminal, but simply Jerk Ass Stu Shepard, who is having an affair and pretending to be a big shot; not exactly what you would call pure evil. Also, the sniper's methods to get criminals, real or imaginary, to confess, including targeting their loved ones, are quite questionable, to say the least. In the end, Stu confesses to his deeds, and the sniper decides to spare his life and those of his loved ones...though it's hinted that the sniper is going to check up on Stu once in a while to make sure that Stu keeps his promise of not being a douche.
In the Cold War political thriller Seven Days in May, General James Mattoon Scott is secretly staging a coup against the President of the United States because he disagrees with the President's efforts to set up a disarmament treaty with the Soviets. Several chilling Breaking Speeches, followed by some equally impressive Kirk Summations, follow toward the end.
General Scott: James Mattoon Scott, as you put it, hasn't the slightest interest in his own glorification. But he does have an abiding interest in the survival of this country.
President Lyman: Then, by God, run for office. You have such a fervent, passionate, evangelical faith in this country - why in the name of God don't you have any faith in the system of government you're so hell-bent to protect?
TRON: Legacy: Clu, in his pursuit for the perfect system, eradicates every single thing he believes to be an imperfection...including the ISOs, which his user believes to be a miracle, and could have very well changed the system and the real world for the better had it not been for Clu's fanaticism.
The Royal Spanish Navy in Pirates of the Caribbean: On Stranger Tides is on a mission to destroy the Fountain of Youth for the same reasons, and shoot one of the English soldiers to begin with.
Transformers: Dark Of The Moon: Sentinel Prime, former commander of the Autobots, is revealed to be this. Originally Optimus's mentor and father-figure, Sentinel had been corrupted by eons of war. Convinced that Cybertron's survival was more important than loyalty to his men, Sentinel struck a deal with Megatron to find another world whose resources could be used to replenish Cybertron. Finding himself on Earth in present day, Sentinel turns on his former allies and joins Megatron to begin making plans to use Earth's resources (in particular, the six billion or so fleshlings they can turn into a Slave Race). Sentinel's Knight Templar status is also revealed to be influenced by his god complex; remembering how the Cybertronians, particularly the Primes, once lived like gods, he is immediately disgusted by how Earth's leaders treat the Autobots as simple machines.
In Star Trek VI: The Undiscovered Country, several Starfleet and Klingon officers conspired to preserve their respective ways of life by sparking a war between the Empire and the Federation. It's often pointed out that in conspiring to prevent Federation and Klingons from ever working together for the common good, the conspirators ironically proved that the Federation and the Klingons can work together for what they perceived to be the common good.
In Man of Steel, Zod believes he's ultimately doing what's best for his people. In fact, due to Krypton using Designer Babies to fulfill roles in their society, he cannot help it.
Zod: No matter how violent, how cruel, every action I take is for the greater good of my people.
A literal version in Kingdomof Heaven; the King's brother-in-law and his right-hand man are actual Knights Templar who also fit the trope to a T. When the king dies and the brother-in-law becomes king, it comes to the point of killing the Saracen leader's sister in order to provoke a conflict.
Battra from Godzilla (in the films) was created by the Earth to be its protector. However, while his intentions are in the right place, his actions are another story. There's a reason Mothra had to seal him away.