Bishop Mozgus from the "Tower of Conviction" arc in Berserk takes this trope to the most nightmarishly horrifying logical conclusion imaginable, having tortured to death uncounted thousands of "heretics" (which, to him, includes such miscreants as peasants desperately begging for food for their starving children when that food was supposed to go to churchmen and church-affiliated knights, who most definitely are not starving).
In Fullmetal Alchemist Scar tries to pass off his murderous revenge against state alchemists as this, saying that their alchemy is an affront to his god Ishval. However, Ed later points out that Scar is deceiving everyone with this excuse, including himself; his real motive is nothing more than simple revenge for the Ishvallan War of Extermination. After this, Scar starts his transformation into The Atoner, fully admitting the crimes he's committed without using his religion as an excuse. It helps that his old master (presumably the guy who trained him as a priest) survived the genocide and when Scar runs into him, he takes the Ishvala Is Love approach—or more like, the Revenge Helps Nothing approach. This is one of the few instances of religion having a positive impact in the setting.
In the English Gag Dub of Ghost Stories, Momoko is a fundamentalist Christian. At times she objects to the magic used to defeat the ghosts, but most of the time she mentally translates "ghost" to "demon" so it's okay, and she insists that her own channeling powers were a gift from God as a result of her conversion.
Alexander Anderson from Hellsing is a good example. He is a Vatican priest who works for the Iscariot branch; his job is to kill vampires and other unholy creatures. Alexander compulsively quotes lines from the Holy Bible when he speaks, especially when facing whom he believes to be a heretic or monster that must be slain. He also has an extreme dislike for Protestants, going so far as to call Sir Integra "Babylon" in reference to "The Whore of Babylon". As bad as he can be, he has honor which transcends it. Father Enrico Maxwell, however, is much worse.
In YuYu Hakusho, the Armed Church of the True Disciples is a fanatical religious sect which believes that the spirit world beings are emissaries from God, preaching a hard-line stance against the Demon World (whose inhabitants are regarded as the spawn of the devil) and who are prepared to fire the Interdimensional Laser at the human world to get their demands met.
Certain recurring characters of Jack Chick's various tracts combine the Fundamentalist with Easy Evangelism. Results are awkward, especially considering that you're supposed to be on their side.
Israeli comic artist Uri Fink created a superhero team of a Jew, a Christian and a Muslim, appropriately named The Fundamentalists. (They're fun! They're mental!) Rather than actually saving people, however, they always end up killing them instead, because instead of fighting crime they violently punish whoever they consider to be sinners, regardless of the sin. Over the course of four stories, they have:
J. Jonah Jameson cannot admit that Spiderman is anything other than a menace even though he has saved Jameson's life dozens of times. Various reasons have been given over the years as to why this belief is stuck in an otherwise good journalist's head, who caught flak several times in-universe for being in favor of mutant rights, among other things: The anti-Spiderman rant sells papers; if Spiderman were to be captured, tried, and imprisoned, the Daily Bugle would fold as soon as the judge sentenced him; Jameson is a muckraker; he's only doing it to boost circulation.
Marianne Bryant, who is the head of a group of religious conservative students. Before setting her sights on Olive, who she (and everyone else) believes has had premarital sex, Marianne petitioned to have the school football team to be renamed to Woodchucks from Devils. Apparently, she picked up the trait from her father, a priest.
Marianne's father is adamant about his own beliefs and doesn't recognize others, as evidenced by his constant corrections of Olive's hypothetical question about Hell. As far as he's concerned, Hell is a real place, and there's nothing hypothetical about it. He's a hypocrite as well; he's watching Olive's webcast, expecting her to have live sex on camera, and is disappointed when she doesn't.
Marianne's hardliner boyfriend Micah ends up with an STD he picked up from the guidance counselor, a married woman.
Nute Gunray from the prequel trilogy era of Star Wars, though he is a political (and economical) example, rather than religious.
Seen in "The Grand Inquisitor," a story within a story in Dostoievsky's The Brothers Karamazov. The eponymous figure, representing a Corrupt Church, effectively tells Jesus Christ to His face that His teachings are no longer relevant to either the world in general or the Church in particular. Christ isn't condemned to death, but He doesn't seem to have much effect on the Inquisitor either.
Margaret White, the mother of Carrie in both the book and the film.
Crusade, the second of David Weber's Starfire books, featured religious zealots who worshipped the Terran Empire as gods, and denounced the Khanate of Orion as devils. Within their society, religious doubt was absolutely not tolerated.
Terry Pratchett parodies the concept of fundamentalism with the Omnians, who cling to their monotheistic beliefs despite being demonstrably wrong. The majority of them are depicted as basically nice people, however, just irritatingly overzealous at times.
Small Gods is the story of how they got past the old fire and brimstone style of fundamentalism. An interesting twist is that virtually none of the people shown in Small Gods actually believe in the Great God Om, rather they believe that they don't want to be tortured by the Quisition for expressing their unbelief.
Vorbis the Exquisitor is perhaps the ultimate fundamentalist. He has no trouble admitting to himself (and a few others) that it is irrelevant if something is empirically found to contradict the teachings of their holy book, because real truth is found within. In other words, even if he's not factually right, he's still right, and right to extinguish those who disagree. And he's not just pretending to believe he is, either, but really believes he's following his god's will. Supernatural beings see his mind as a steel ball; nothing can get in or out. Of course, when his actual god appears in an admittedly unlikely physical form in front of him, he can't hear him at all, as any believer could. In the end, after his death, he finds himself in the desert where several of his victims have also found themselves. They actually found it to be a hopeful new start. He can't cross the desert because the desert is what you believe, and he finds it horrifyingly empty.
"Fundamentalist" atheists, of course, are equally deluded... seeing as the gods have tendency to come and throw lightning bolts at you if you refuse to believe in them. The golem constable in the Watch, Dorfl, being ceramic and thus fireproof has proven to be something of a challenge in this regard.
Good Omens: Sergeant Shadwell hates all Southerners, and, "by inference, [is] standing at the North Pole." Thinks Aziraphale is a Russian spy and Crowley, because he wears sunglasses, must be a member of the mafia. Also believes his landlords, the Rajits, practice voodoo, and frequently condemns his neighbor across the hall, who performs seances and entertains gentleman callers as a "Painted Jezebel" or "Whore of Babylon." He also hates witches. And Go- Sa- Somebody help you if he suspects you don't have the correct number of nipples.
In Death: The murderer in Vengeance In Death is definitely this. Eve even refers to him as a Bible-thumper close to the end of the book.
The Christians from the Left Behind series. They engage in selfishness, pettiness, and condescension to anyone who doesn't agree with them. That sort of behavior is expected from the bad guys, the followers of The Antichrist, but these are supposedto be the heroes and the audience is supposed to be on their side.
Outbound Flight: Jorus C'baoth is a Jedi version of this. Very few of his fellow Jedi get along with him as a result, and the only one who can really knock sense into him is Yoda.
In one of the short stories Philip Jose Farmer wrote in the Riverworld series, Jesus Christ and Tom Mix run across a territory controlled by an Inquisitor. The ultra-fundamentalist Inquisitor ends up burning Jesus Christ as an anti-Christian heretic.
The novel Towing Jehovah revolves around the discovery of god's body, and a group of atheist fundamentalist extremists attempting to destroy the body to get rid of any evidence of his existence.
For a series with a lot of religious beliefs on display, Babylon 5 largely averts this trope. Political zealots are fairly common, however, and the conflict between the Vorlons and the Shadows boils down to diametrically opposed doctrine.
Sheldon Cooper applies this attitude to everything, right down to people's favorite flavor of pudding: Raj is "axiomatically wrong" to prefer tapioca, because the best pudding is chocolate. Period. This attitude makes him a far, far worse scientist than he thinks, as he refuses to even consider any criticism of his methods or results.
Sheldon's mother, by contrast, is a classic Christian fundamentalist at the opposite end of the spectrum. However, as opposed to most Christian versions of this trope, his mother is hardly a ranting lunatic and is Actually Pretty Funny.
Sheldon: I'm going to stay here in Texas, teaching evolution to creationists. Mary: Watch your language, Sheldon. You know everyone is entitled to their opinion. Sheldon: Evolution is not an opinion, it's a fact. Mary: And that is your opinion.
Agent Nelson Van Alden from "Boardwalk Empire" is this to a terrifying degree. Towards the end of the first season, he attempts to convert a subordinate, who is Jewish (and also possibly get a confession of murder out of him; it's not quite clear) by 'baptizing' him repeatedly in a river, and ends up drowning the guy.Word of God says this was unintentional, but he sure doesn't seem too sorry. He also cheats on his wife, which is not very Christian, although he does it while wearing a "What Have I Done" expression.
Shirley in Community is a Christian fundamentalist who is shown early in the series forcing her beliefs on other members of her study group. Most attempts are rather mild, like mandating wearing "What Would Baby Jesus Do?" bracelets. There are other instances hinted at that aren't so benign, like inviting Annie to a pool party which turned out to be an involuntary baptism. Later episodes have toned this down considerably, and ultimately Shirley is shown to have many good qualities that outweigh the bad.
The Proclaimers' song "The Light" is a scathing condemnation of the real-life examples of this trope from a moderate Christian perspective, with lyrics such as "I believe in God alright/It's folk like you I just can't stand."
In Exalted, the worst of the Immaculate Order combine this trope with Arrogant Kung-Fu Guy. Most notable is the signature character Peleps Deled, who once killed a fellow monk...for suggesting that an old, obscure, hard-to-translate passage of the Immaculate Texts read "from the Dragons" rather than "of the Dragons". This is a minor instance of dog-kicking for him.
In In Nomine, Khalid, the Archangel of Faith, goes through this for a few centuries, becoming increasingly devoted to a xenophobic, fundamentalist interpretation of Islam. He was very nearly setting himself up for a Fall when a near-miss with Armageddon shocked him back into a more open, accepting mode.
In Magic: The Gathering, White embodies the positive aspects of peace, order, and stability, but its negative side is expressed through this and the Knight Templar, seeking to purge any who disagree with its dogma. The card True Believer exemplifies this aspect of White, especially in its flavor text:
So great is his certainty that mere facts cannot shake it
A lot of the human characters. Presumably, some of the Chaos-worshipers too, but they're less about "proving you're wrong" and more about "tearing your head off and doing something obscene with the neck-stump". Of course, given the Your Emotions Make It Real and Clap Your Hands If You Believe nature of The Warp in that setting, willful ignorance and blind faith in The Emperor are something of a survival mechanism for humans in that universe.
The Church of Unitology seems to run on fanaticism, but the best in-game example is the insane, homicidally devout Dr Challus Mercer.
Subverted in his former fellow-believer Dr Terrance Kyne, who starts out that way but has just about reasoned himself out of his zealotry in the face of overwhelming contradictory evidence by the time the player meets him.
The Qunari of Dragon Age are fundamentalists by definition. Only those who dogmatically follow the Qun are actally called Qunari. If they deviate from the demands of the Qun then they are declared Tal-Vashoth instead. Interestingly, anyone who is not of the Qunari race (i.e., the Kossith) can still become Qunari by following the Qun. The Qunari don't discriminate based on race, only beliefs and magic. Anyone who doesn't follow the Qun is simply bas ("thing").
Halo: The Covenant is full of these, though some of its leadership has been portrayed as more opportunist than fundamentalist.
Pokémon Black and White: Team Plasma are a non-religious example. They even regularly chant "we are right, everyone else is wrong!". Explored in that their actual goals are pretty noble (even the protagonists acknowledge this), but their arrogant denial of everyone else's views makes them come off as villainous anyway. (also Lampshaded). It ultimately turns out the Big Bad who made the organization doesn't believe in its goals at all and just wanted to Take Over the World.
Sister Miriam Godwinson from Sid Meier’s Alpha Centauri is a fundamentalist when it comes to religion and saving souls, and a subversion when it comes to technology. She appears to be an anti-tech fanatic, but she's actually calling for restraint, reason and ethics in a scientific field dominated by the amoral University. This is somewhat flanderized in the novel Twilight of the Mind by Michael Ely: Miriam thinks that all technology is evil, unless, of course, the "righteous" use the same technology to enact God's will.
Claudia Wolf in Silent Hill 3, to the point where she murders Vincent, a fellow cult member, just for disagreeing with her.
Before that the series had Dahlia Gillespie, who was so wholly devoted to the cause that she turned her own daughter into an Apocalypse Maiden via a near-deadly ritual and left her trapped in an endless nightmare of physical and psychological pain for seven years afterwards, all for the sole purpose of strengthening said daughter's inner hate so she could birth God and whisk them all away to Paradise.
StarCraft II introduces the Tal'Darim Protoss, an even more fanatical sect of their race.
SWAT 4: The Children of Taronne. Your SWAT team has to bring in this cult who have bombs that will blow up half the city, and the cultists have no regard whether their gunfire will set them off. There's insane writing everywhere, cultist material, children's rooms but no children. Even your teammates get freaked out at the religious babbling. Then you get to the basement. The cult had dug up the basement ''and buried their murdered children in graves,'' in preparation for the holocaust the cult believes in. Watch it here if you dare, a few Lets Plays of this level had actually caused Heroic BSOD.
A benevolent example is Mother Helen of Dead Island. Highly religious and invoking her (possibly monotheist) religion constantly, she believes the outbreak is The End of the World as We Know It. It's because of her beliefs that she sets out to help anyone she can and her quests are either to help her do so or to set things right for the coming apocalypse.
Charlotte from Penny and Aggie. Though she's changed since developing an interest in the only black - as well as Muslim - student at the school. As well as in the aftermath of having fallen afoul of the machinations of the one cast member who is truly, unrepentently, sociopathically evil.
America, particularly when it comes to his opinions on homosexuality. He'd be more effective if a) his sister wasn't pro-gay rights (and a shipper), b) Sweden (the target of his ranting) actually knew what God was, and c) he didn't think gays were flamingos. (Then again, Sister America thinks they're penguins.)
The Faroe Islands also has shades of this. A pity he was just as turned on by Denmark/Netherlands as Sister Japan was.
Sinfest: Seymore and Lil Evil, for Christianity and Satanism, respectively. It's quite clear their respective deities can't stand their fundamentalist cheerleaders. Especially anvilicious in the case of the former, portrayed as a robed stick-figure with a fake wire halo. Frequently in his mania for collecting all things Jesus-related he often fails to notice that Jesus is standing right there. Like the other characters, he also has a feudal incarnation as a Buddhist Monk, generally retaining all his other characteristics. Surprisingly, this is occasionally subverted when Seymore does something genuinely kind and compassionate. Although anything vaguely kind Seymore has ever done has gone right out the window after he Took A Level In Jerk Ass in Bad Behavior.
Virgo from Zodiac, though she tries to avoid being judgmental.
Dolly in 80's Dan turns out to be like this, but just when it comes to Christmas.
Rachel Gettys of Survival of the Fittest v4 is your standard Christian fundamentalist along with showing Rich Bitch traits. She spends a good amount of time on the island hallucinating "visions from God" and trying to convert people. Disagree with her and she'll bash your head in.
The Simpsons: Ned Flanders due to Flanderization. Which is a shame, because he used to have sort of a cult (pun unintended) fanbase among religious viewers for representing everything potentially good about Christians (nice to a fault, accepts everyone, strong family values, etc.), even if it was taken to a humorous degree. In more recent (read: at least 15) seasons the writers have just used him as a strawman for Moral Guardians. However, averted in The Simpsons Movie, where he's shown as a more fatherly figure and seems to fully revert to his season 1 kindness (and then some).