Hero House has Kratos, who seems to have taken his God-slaying mission across multiple dimensions, targeting even Superheroes in his quest.
In The Gamer's Alliance, the Clergy of Cardia and later the Church of the Memory of Cardia who follow the God of Order show signs of being knight templar in their quest to hunt down anyone who is worshipping Mardük the God of Chaos or collaborating with demons whom they see as abominations to be purged.
The Mujahedin, from the Global Guardians PBEM Universe, are Islamic superheroes who use Shariah law as a guideline to how much force to use against the criminals they face...which means that they kill a lot of criminals. They're also fairly harsh against non-Muslims, liberal Muslims, and anyone who thinks the Mujahedin crossed the Moral Event Horizon a time or two. They also fall squarely into the realm of Your Terrorists Are Our Freedom Fighters when it comes to their views on Israel.
Most worshippers of Khersis in Tales of MU come off this way towards the main character as a result of Fantastic Racism, owing to the fact that she's a half-demon and their god's portfolio includes protecting humanity from demons.
The incipient paladin Gloria from her mixed melee class comes off as this, as well. Her characterization starts off painting her as just another run-of-the-mill fundamentalist, but when she starts to engage in activities that might seriously harm Mack, like sanctifying herself before battle and uttering prayers as Mack goes to meditate, which may indicate a slippage towards Black and White Insanity, she becomes this.
The emancipated golem Two also comes off as this in a much less malicious way. She has a pathological desire to do as she is told, and so she takes rules very seriously, sometimes to such a degree that she causes problems for herself and her friends.
Don Cheadle's funny and yet at the same time creepy take-on of Captain Planet in Funny Or Die.
By the end of The Anglo/American Nazi War , the victorious post-war Allies are so horrified by the death and destruction caused that they enact a policy of using any tactic to stop anything that might balloon out into World War III. Unsanctioned space launch? That means you might have access to ICBMs, and the A4 can't have that. Sectarian violence in the third world? Send in the troops and attack both sides. One of the fifteen Administrative Regions which make up what was once the Reich try to push for the reunification of Germany? Nuke the place from orbit and kill everyone in it.
Filbert in Ruby Quest went totally off the deep end when the Metal Glen fell apart due to their use of the Cure (which turned out to be part of an Eldritch Abomination). He currently believes that there's an infection ravaging the facility, and that he's the only one clean. He's totally clean, and he'd like you to be too. Just sit tight while Filbert cuts the bad out of you...
In Void Domain, when it comes to anything they consider a possible enemy, the Elysium nuns tend to shoot holy lightning first and ask questions never. Taken Up to Eleven by Sister Cross, who thinks nothing of surprise-attacking a blind girl in her bedroom, then attacking a teacher who comes to her defense.
The nation of Wreathe in Mortasheen is basically the Enclave turned Up to Eleven. They are so obsessed with a "pure" humanity that they launch unprovoked attacks on anything even slightly unhuman, and are more than willing to murder other humans who refuse to bow down to their totalitarian regime. The fact that they're secretly lead by a batshit insane computer program doesn't exactly help either.
In Mahu's "Second Chance", the Zracon are an alien example of Knight Templars. Focused on their crusade to rid the whole galaxy of the influence of the dreaded "Shadow", they will brainwash, conquer and slaughter without a single doubt in their minds. After all, no matter how cruel their actions that, they believe the second coming of the shadow will be far, far worse.