Beware. The word "cult" is very loaded, carrying severe negative connotations. Its value-neutral dictionary definition is just "a new religion." New religions, almost by definition, have questionable legitimacy (they're untested, after all), and aren't very well-established. Added to that, you have the disadvantage of the related prophet or messiah having been alive in living memory, or worse yet, still alive and wandering around potentially saying/doing embarrassing things this very moment. Of course, members of new real-world religions tend to respond badly to anyone calling it a cult. Like, say, Moonies or Scientologists. This is simply an example of words being misused in a political context, like 'Liberal' or 'Fascist.'
In fiction, cults tend to follow a few specific forms:
Second Coming: More accurately billed as a sect, as its beliefs are rooted in an existing religion, this is a group led by an individual who lifts himself up as the rebirth of Jesus Christ (or another important religious figure).
Alien Worshipers: Dogma based on popular modern myths, with beliefs and practices grounded in sketchy science and misconstrued theory more than spirituality.
Revivals: Base their beliefs on old religions no-longer practiced.
Yiliaster from Yu-Gi-Oh! 5Ds Is somewhat similar to the two mentioned above, but they don't recruit members and are hinted at being much more powerful.
The cult revolving around "Friend" in 20th Century Boys. This begins to change as the cult forms the Friendship Party of Japan and initiate a totalitarian takeover of the Japanese political system and, eventually, that of the rest of the world.
The Lemures of Baccano!!, who worship the immortal Mad Scientist Huey Laforet. They believe that if they serve him, they may obtain eternal life for themselves. Huey is not actually capable of making others immortal, and regards them with amusement and scorn for believing this.
In the novels, there's SAMPLE, a cult that worships pain. They designate a child as their "sacrificial god," then brutally torture the child, supposedly as a means of having them take on all the pain the worshippers would be feeling instead.
Ai Kora has a truly bizarre example, the Church of Bluish-Purple, run by a loony with a fetish for bloomers (as in buruma, super-short girl's gym shorts).
An example appears in Pet Shop of Horrors: Tokyo, but it's hard to tell if it's a straight example or subversion. In one of the stories, a teenage delinquent is accepted into a group led by a woman claiming to be an Angel. None of the girls do anything wrong, as everyone says: they do community work, farming, visit the sick and elderly...the only law seems to be that the girls must give up their cellphones and never eat a bird. Suddenly, all of the girls drop dead, seemingly at the exact same time, and their leader is nowhere to be found. However, it turns out that they all died of grief after learning the food they ate was contaminated and accidentally mixed with chicken meat. They were so horrified that they ate bird, they all dropped dead at once. Count D says he firmly believes the leader was an angel who took the girls to Heaven.
One drives the plot of a Franken Fran chapter. A man comes looking for his missing daughter, having gotten a lead suggesting they might know something about what happened to her. It eventually turns out that she was kidnapped and ended up becoming their messiah figure, but she fell ill, so they brought in the eponymous experimental surgeon. Fran saved the girl's life by converting her into an enormous factory, with her physical body reconfigured to be hooked up to the facilities. The stereotypical low-pay work the cultists were doing was running the machines that stood in for her digestive, endocrine, respiratory, and reproductive systems. Yeah, reproductive. She's pregnant, at age ten, on top of everything else.
The Cult of the Sacred Eye plays a major role in Mirai Nikki, as the Sixth Diary Holder is the leader of said cult. She is worshipped by them as an oracle, and has lived in the temple complex for almost all her life (she herself is well aware that she isn't an oracle, but plays the part because that's what she's done all her life). Revealed later to be a hoax started by her parents when she was a young child, and after her parents were killed in a car crash, the other leaders of the cult imprisoned her and used her as a Sex Slave. It's not made clear exactly how she regained control of her followers since then.
In the manga Arisa, the titular character's class has been sucked into a cult revolving around "The King" whose followers text him their wishes, and each "King Time" he selects one to grant.
Afterschool Charisma (aka Japanese Clone High) has a bizarre cult that takes root among the clones lead by a clone of the legendary 3rd century Japanese witch-queen Himiko who worship the spirit of Dolly the Clone Sheep. Yeah.
In Kotoura-san, Hiyori's family run one in the manga, named after their family name. The anime changed it into a dojo.
Back during the Dan Jurgens-era of Superman, there was a cult of people who praised Superman like a God. It wasn't something he liked. After Superman died, they began seeing him as a more messianic light, waiting for the day he would rise from the grave. And when four people bearing the S-Shield rose, factions took hold, each one rooting for the four bearers. It got to the point where Maggie Sawyer started to worry that a gang war of sorts would break out between the four.
Karkat is worshiped by the titular Cult, as they believe him to be the Sufferer's reincarnation (which may or may not be true, though Karkat himself strongly denies it). He dislikes this- with good reason; they forced him to act as their messiah, and his duties involve spreading a lot of ridiculous propaganda- but admits that just being a normal cultist would be a pretty good life.
In Camp Nightmare, the alleged day camp is actually a front for a very wide-spread cult.
In Guards! Guards!, Ankh-Morpork is revealed to be rife with tiny little cults who are ostensibly trying to bring their dark god to power (so much so that a cultist actually gets about halfway through an extensive password routine before it falls apart and the guy behind the door realizes he's got the wrong address); most of them just wanted to add a little mystery to their lives to impress chicks, though.
The young adult book Leaving Fishers is about a cult with high-schoolers. They claim to be a religious group, but their methods are clearly abusive. (One character tells a cult-investigation group about them, and learns Fishers meets every single trait of cults.)
The Order of the Rings of God in Faye Kellerman's Jupiter's Bones.
When you get closer to its core membership, The Sharing in Animorphs is constructed much more like a cult than the all-ages scouting program it pretends to be.
Subverted in Maggody and the Moonbeams, where a reclusive all-female Christian sect is actually a front for a group of battered women in hiding, whose members are being exploited for cheap manual labor by their corrupt leader.
Petaybee: Shepherd Howling leads a doomsday cult that encourages pedophilia and other interesting forms of child abuse.
The Subject Steve: The Center for Nondenominational Recovery and Redemption could be described as a cult and a rest home, combined.
The Mysteries from Elantris are a cult that spun off from the benign Jesk religion- where Jesk worships a Force-esque life energy called the Dor, followers of the Mysteries seek to manipulate it to their advantage. The Mysteries is characterized by secrecy and bizarre rites that sometimes involve Human Sacrifice- as such, it's not very popular and tends to exist only in small, secretive groups.
A rare positively portrayed example in Octavia Butler's Parable series. The main character, Lauren Olamina, starts a cult called Earthseed which believes that God is change. They are persecuted by the Christian America sect, which probably fits more of the cult stereotypes.
In Oryx and Crake and The Year of the Flood, it's clear that most people in-universe see the God's Gardeners as a cult. Whether or not it really is a cult depends largely on the reader's perspective, although parts of the latter book told by members of God's Gardeners provide a more nuanced view.
There is also a New Doctor Who book which features a cult based around a horrible picture of a clown. The whole book is, essentially, a very paranoid and more than slightly creepy rant about religion (but specifically Christianity). The book's entire message is, literally, "Be very very afraid of what I imagine religion to be".
The followers of R'hllor in A Song of Ice and Fire throw people into fires as sacrifices and claim to see visions in fires. This is in total contrast to the very mainstream fantasy counterpart religions of Faith Of The Seven, also called the New Gods (Catholic/High Church of England) and worship of the Old Gods (a naturist religion).
The second novel in Taylor Stevens' Vanessa Michael Munroe series, The Innocent (2012) has Munroe infiltrating a cult called the Chosen of God to rescue a child who was forced into its ranks eight years earlier, and has since been subjected to brainwashing and repeated sexual abuse. This cult is a thinly veiled Expy of the Children of God, which Stevens herself was born into and escaped from, after which she completed her education and turned to thriller writing.
The Patron Saint of Butterflies by Cecilia Galante is about Mount Blessing, which is a religious commune in Connecticut led by the charismatic leader Emmanuel. Agnes loves the cult, meanwhile her cousin Honey rebels against its strict rules. Their grandmother, Nana Pete, who isn't in the cult, takes them away from the cult when Emmanuel refuses to send Agnes' seriously injured brother to the hospital. The book is based in the author's childhood experiences in a cult.
In Converting Kate by Beckie Weinheimer, the protagonist Kate was raised in the Holy Divine Church, but leaves it after her father's death.
The Surivors in CHERUB are a cult that is an offshoot of Christianity, linked to an eco-terrorist group called Help Earth. They have a fortified and armed compound in the middle of the Australian outback, where they further brainwash the most intelligent children of cult members. This compound is destroyed at the end of the book.
The Luskentyrians in Whit or Isis Among the Unsaved by Iain Banks is a small cult based in a farmhouse in Scotland. Although the main character is a True Believer, she's also intelligent and insightful enough to recognise that, while the cult's founder (her grandfather) is obviously the Chosen of God, he's also a bit of an old rogue. It turns out he's much more of a rogue than she imagined, while at the same time less of a fraud than the reader might expect. He really did have a religious experience, and devoted the rest of his life to figuring out what it meant. It's her brother who wants to turn it into a Scam Religion.
Live Action TV
On Stargate SG-1: the Go'auld Seth, after spending a long time as a disembodied symbiote in a canopic jar, takes a new host and tries to found a new religion to worship him as in days of old. The cults he founds always end up either being disbanded by the police or committing mass suicide, with Seth escaping in yet another new host; this pattern is how SG-1 and Jacob find him.
Law & Order, during an investigation of a bombing, turned up a cult in the middle of Manhattan worshipping a con-man as a new messiah. He was a semi-delusional fraud; as he was convicted, he used thumbtacks to give himself stigmata. His entire "flock" killed themselves hours later.
Between the original show and the Law & Order: Special Victims Unit, the good guys have encountered several cults; the SVU episode "Charisma" had a particularly heinous one. When a pregnant preteen girl is brought to the hospital, a path is traced to a cult she's a member of. During a standoff at the start of the episode, all the children in the compound are killed by its leader. In the climax of the episode the pregnant girl threatens to kill Olivia if she tries to stop him and cannot be talked down. A horrific ending (as Olivia might have to shoot the child to save herself) was barely averted because the leader claimed in a rant he was greater than God - the girl killed him instead.
Sabrina the Teenage Witch had a cult around a fake "witch" who also hoarded its members' worldly possessions. (And made them eat mungbeans.)
Glory (the Big Bad of season five), being a god, naturally had a cult who worshiped her, even though she was an evil, de-powered and kind of obnoxious god. And her followers were mostly barely-competent minor demons.
"Lie to Me" included a cult of teenagers that worshiped vampires.
"Reptile Boy" had fratboys who serve (girls to) a demon.
In an episode of Everybody Loves Raymond, Robert gets suckered into a lame but loving cult, but is horrified to discover that they too like Raymond better.
In Star Trek: Deep Space Nine, Gul Dukat, a Cardassian who hates Bajorans, forms a doomsday cult based on Bajoran religion in an attempt to kill a few of the people he hates. His plan fails, though, when his followers question his reluctance to metaphorically drink the Kool-Aid first.
Actually, the cult already existed. It's not a Doomsday cult; it's one that worships the Pah-Wraiths because they have lost faith in the Prophets following the Occupation, believing therefore that their Pah-Wraith enemies might not be so bad after all. He just subverted it to his own ends, claiming that the Pah-Wraiths were giving him visions. They actually were, and so the Kool-Aid may really have been their idea. The Pah-Wraith really are evil, and the cult are just mistaken.
The titular Millennium Group in Millennium, at least in the second season and parts of the third.
A subversion appears in the first season of Veronica Mars. Secrecy (sort of), organic diet, isolation, authority clash... and they're actually decent people, whose "secret crop" is Christmas poinsettia flowers. The kid VM "saves" is "deprogrammed" back into a jerk, though she learns about his real soft spots and he remembers her somewhat fondly from her time infiltrating the cult, making him a useful source of information in a later episode.
Uniquely enough, Veronica Mars is one of the few shows to depict a not evil cult.
Neighbours had some of the characters drawn into a cult that was very much a Brand X version of Scientology, which turned out to be the work of a con-man who became a recurring villain.
Ryukendo has the whole town temporarily turn into a UFO-worshiping cult in one episode, complete with dancing and chanting. It turned out to be a trick by the Monster of the Week, but they weren't aware of that.
The X-Files had so many examples it would be best to designate between straight and subversion:
Straight: A Satanic cult made up of the members of a small town PTA ("Die Hand Die Verledzt").
Subversion: A vegetarian cult that believes in "walk-ins" (moments of spirit possession) that turns out not to be tied to the abduction, drugging, branding, and inoculation with extraterrestrial DNA of a group of small town teens ("Red Museum"). They were connected, though somewhat indirectly. The Cult's founder was involved with the conspiracy, and enforced vegetarianism because the conspiracy was running a secret experiment involving the town's meat supply and they needed a control group.
Straight: A doomsday cult that believes in reincarnation and ends up taking part in a mass suicide ("The Field Where I Died").
Straight: A murderous cult that worships a slug-like parasite that they believe to be the Second Coming of Christ ("Roadrunners"). No, seriously.
An episode of Cold Case dealt with a cult that preached a new beginning by eliminating the past; in a slight subversion, instead of a mass-suicide, the cult was planning mass-patricide, killing their fathers as a tribute to their "new" father figure, the cult's leader.
An episode of Monk had the eponymous OCD detective infiltrate and get completely sucked into a cult, whose charismatic leader is played by real life OCD sufferer Howie Mandel. Humorously, while Stottlemyer's partner Randy and several other characters were trying to deprogram Monk, Monk manages to convert Randy. In a plot twist double-whammy, Monk manages to both alibi the cult leader and break up the cult: the leader claimed that he was never, ever sick, but on the night in question he was secretly receiving cortisone injections to deal with back pain. The cultists, upon discovering their leader is a fake, simply abandon him. Even liars sometimes speak the truth. For some reason Monk seems not to have appreciated, afterwards, that however dishonest the cult leader might have been, he had more success than Dr. Kroger ever had had in helping Monk overcome his OCD.
Nina on Just Shoot Me! once belonged to a Moonies-like cult called the Church of the Rising Star. It has been suggested throughout the series that Nina has belonged to various other cults.
The Church of Synthiotics in Wild Palms, with its "New Realism" philosophy.
The Touched by an Angel gang encountered one and revealed themselves when the leader was about to commence a mass suicide in response to authorities arriving. Monica convinces everyone to leave instead; the deluded leader starts a fire in response. The angels rescue everyone but him, as he refuses to accept their help.
In Boy Meets World, Shawn joins a cult who convinces him to give up all his friends. He leaves when Mr. Turner is in a motorcycle accident, and the leader wants Shawn to not see him, so he rejects the group.
Other than that, it's very non-cultish. The Center isn't difficult to locate, there's no chanting or monetary aspect, and everybody appears well rested and nourished. They even have video games.
An episode of CSI Crime Scene Investigation had the team investigate a cult-induced mass suicide. The sole survivor found out the leader was a fraud and killed him. She couldn't bear to tell the others the truth, so she let them die.
Parodied on Strangers with Candy in the two-part episode "Blank Stare," where Jerri is lured into a "collective cooperative community service operation outreach program project." The leader/messiah of the cult ends up hating her so much that he forces her to leave despite her enthusiasm and willingness to assimilate.
Joey was a part of a cult but "Five hundred bucks to get to level 3? Forget it!"
Echo infiltrates a Branch Davidian style cult in the Dollhouse episode True Believer, with an outcome similar to that in Waco.
Home and Away has had a couple of cult stories. The one from more recent memory involved Tash getting involved with The Believers, whose leader had a prophetic dream involving her and her then-unconceived child. Which meant that the plan involved the leader's son getting Tash pregnant with her daughter Ella.
On Community Pierce insists that he is a Buddist but the rest of the group keeps telling him that he is actually in a cult.
In Volume Five of Heroes, we are introduced to Samuel Sullivan, who runs a carnival that is essentially a cult for "specials."
"The Ugly Ducklings" are the focus in two episodes on Kamen Rider Fourze lead by a ballerina who worships a Zodiarts known as Cygnus and where other students do good deeds which is valued on a point system. One of those members actually is Zodiarts and the cult—being stupid—forces him to transform into Cygnus. They disband after that.
In the Starsky & Hutch episode "Bloodbath", Starsky is abducted by the followers of the memorably creepy Simon Marcus.
In the Mr. Show episode, "Heaven's Chimney," David has apparently joined a cult lead by "The Bob [Odenkirk]" and is planning on "going up Heavey's Chimney." Tom Kenny and a few other cast members have to deprogram him. Said sketch also included the cult's greeting "Terra-da-loo!" which fans of the show tend to quote frequently.
From The Following: Serial Killer Carroll's titular following. He prefers to think of them as his friends. It begins to fall apart shortly after he escapes from prison and takes control of it, since it's members are all psychos.
Debra Parker, Hardy's new superior, keeps on telling him not use any word relating to the word cult, and doesn't want the FBI to label it a cult, noting the implications it carries. He later finds out she's the head of the FBI cult (Alternative Religions) unit. Then it turns out she was raised and abused in a cult herself.
On The Listener the IIB investigates the death of a cult member. The cult itself turns out to be mostly benign and the killer turns out to be a crazy member of the group who took it's message way beyond what the leader intended. The leader even admits his insistence that his followers cut all ties to their past was a big mistake and works to make the group less insular.
Dogbert in Dilbert started his own cult on one occasion:
Dilbert: I think you've taken this cult idea of yours too far.
Dogbert: Who says it's a cult?
Dilbert:You said it's a cult!
Dogbert: That word has a bad connotation. I prefer to think of it as a bunch of morons who have nothing better to do with their lives.
Basically any stable ever run by Raven has been one of these, be it in WCW, ECW, or TNA. Some are more insane than others, such as the rather Narmy Serotonin.
Back during the Attitude Era, the WWF had The Undertaker's Ministry Of Darkness where Taker would go kidnap C-level guys on the roster and "convert" them into his followers with new names. There was also to a lesser degree The Brood, who were briefly part of the Ministry themselves.
The Wyatt Family have some very creepy cult-like trappings to their gimmick, although the word "cult" has actually been used overmuch concerning them. Wyatt himself comes across like a mash-up of Azazel, Max Cady, and Charles Manson with his deranged promos, and he's accompanied by two devoted "sons" (Luke Harper & Erick Rowan) that obey him without question.
The Order of the Neo Solar Temple in CHIKARA. Led by UltraMantis Black, they've been known for brainwashing and converting enemies. The crowd usually bows to them when they enter, even.
In the skirmish game Necromunda, using a 40K variant and set on the eponymous planet, a player's force could belong to the Redemptionist Crusade, a sect that relates to the normal Emperor-Worshipping Imperial Citizens (you know, dogmatic, intolerant, heretic-burning, etc.) about in the same way that David Koresh-style sects relate to standard Evangelical Christianity. They are TOO fanatic even for Imperial Society, and hence are outlaws to be killed on sight.
In Sandy Mitchell's Ciaphas Cain novels, a footnote mentions that a cult worships Cain as the physical embodiment of the Emperor's will — something that would have horrified him if he ever found out.
'Then the prophet spake: saying
"Frak this, for my faith is a shield proof against your blandishments".'
Alem Mahat, The Book of Cain, Chapter IV, Verse XXI
The Adeptus Mechanicus worships a living machine for a god. But it's okay, really, because it's an aspect of the Emperor. They're probably not fooling anybody, but nobody wants to piss them off too much since they're pretty much the only ones who know how to use most of the machines and have their own in-house paramilitary forces to boot. The fact that they might actually be worshiping the Void Dragon and this being Warhammer, probably doesn't bode well.
Also extant in Exalted. In its setting, the term "cult" is value-neutral, though. The makers even said in one book that if the word had the same negative connotation in Creation as it does in real life, many organizations normally calling themselves cults would vehemently deny that they were such.
There is actually a "Cult" background, which specifically refers to your character having worshippers. Some, most notably the Alchemicals, try to dissuade them. Pretty much everyone else responds with "w00t, free motes!" The main cults not directly related to worshipping Exalts are typically devoted to Yozis, local deities, or their ancestors, and one signature character - the deathknight known as the White Walker or Harbinger of the Ghost-Cold Wind - has dedicated his existence to forcing a fair arrangement on both sides.
The same applies in RuneQuest, older by about 25 years; practically every resident of Glorantha joins a "cult" of one of the hundreds or thousands of gods, and gains some magic from that god. Even the state religion of the Lunar Empire is technically a "cult".
Very common in Dungeons & Dragons (though evil gods who are actual gods—as opposed to demons or devils—tend to have organized churches). Most recurring Arch-Devils and Demon Princes have their own cults, as do certain powerful elementals and other pseudo-deific entities.
One of the very first D&D adventures, The Temple of the Frog, concerned a raid on the cult of an evil amphibian-god.
The 3rd Edition version of the Deities & DemigodsSourcebook, which contained guidelines for designing religions and godly pantheons, described the dwarven earth goddess Dennari, whose followers were described as a benign Mystery Cult.
The Mook level monster in Arkham Horror are Cultists, specifically Cultists dedicated to awakening whichever sleeping God is trying to wake up and destroy the world this session. They usually have a few extra rules that change depending on which Ancient One is in play. Examples Cthulhu's worshippers are particularly grotesque and horrifying, Hastur's ride flying monsters, Nyarlathotep's are without number, etc
The Cabal in Blood, and 100 years later Cabalco (essentially the same cult disguised as a multinational coporation).
The ancient Pagan-Supernatural-Judeo-Christian-Kabbalistic mishmash cult from the Silent Hill series. Though it's rather overlooked in the second game, the first game explains it in great detail, and in the third game, being a chronological sequel to the first, that same cult becomes a very important part of the storyline.
The cult in Guardians Crusade screams of evil but never actually does anything bad... until a certain point later in the game. From this point, the player can (optionally) return to towns from earlier in the game to stop the cult members that have transformed into optional bosses.
Thief II: The Metal Age revolves around the apocalyptic Mechanist cult which has schismed from the Pseudo-Catholic Hammerite church.
Spiderweb Software's Exile/Avernum III allows you to join an anti-magic cult. If any of your characters have magical abilities, they give up their use permanently. This choice makes the game a bit more difficult, and in particular prevents you from stopping a plague of cockroaches, since you can't cast a fireball spell. However, you can always do that quest before joining the cult. The Anama appear again in Avernum 5.
The Happy Happy Religious Group headed by Mr. Carpainter from Earthbound, which kidnapped Paula and was obsessed with the color blue. The quest that involves them would also mark the Start of Darkness for Pokey, which would ultimately see him becoming The Dragon to Big Bad Giygas, and later becoming a major villain in Earthbound's sequel, MOTHER 3, as well.
Subverted, in that Kane and his followers did, in fact, ascend. Also, given how open with their views they eventually became, Nod began to move from cult to religion between the Tiberiun Sun and Tiberium Wars.
Fygul Cestemus from Soul Calibur, who were responsible for the creation of Astaroth, and for turning the Spartan warrior Aeon Calcos into Lizardman.
The Fellowship in Ultima VII. The entire cult is modelled after the Church Of Scientology, from the founder and leader who bears more than a passing resemblance to L. Ron Hubbard, to the obviously rigged personality test the Avatar receives early on.
The Brotherhood of the Dark Rapture from Clive Barker's Jericho, a cult dedicated to unleashing the malevolent Firstborn unto the world.
Team Aqua and Team Magma of Pokémon Ruby and Sapphire, to the point where they are thought to actually be a cult villainous group.
Pokémon Diamond and Pearl's Team Galactic, whose leader wishes to remake the universe in his own image, and whose primary targets are essentially the Pokemon version of gods, are actually more closely related to the thug like Team Rocket than cult like Magma and Aqua. Most of the Mooks you encounter are unaware of Cyrus's goals. In contrast, every member of Teams Magma and Aqua are aware that succeeding in their plan will result in the world being flooded/dried up.
The Children of the Atom in Fallout 3, a group of people in the Town of Megaton who worship the giant unexploded bomb the town is named for. Their essential belief is everytime a nuke explodes a new universe is created. They're obviously crazy, or at the very least completely unaware of exactly how the bombs work which isn't surprising considering there aren't many people left who can properly explain how an Atom bomb works to them. Despite their obviously nutty beliefs they're quite harmless and the residents of Megaton tolerate them, even if most of them think they're nuts. The even gather round at times to watch Confessor Cromwell, the Church's leader, preach about how the bomb is so great! Probably because its good entertainment or they're one of his followers. Even if you effectively disable the bomb Cromwell continues to preach about its gloriousness. Of course, blowing up the bomb and killing him and everyone else, according to him, would probably be a blessing to everyone.
Lampshaded in-game, where the sign that points to the Church building in Megaton reads 'Local Cult'.
The Children of Atom take a nasty twist in the DLC Broken Steel, when one of the high-ranking members starts Stealing the Aqua Pura destined for megaton, and then irradiating it to lethal levels.
The original game had the Children of the Cathedral, a front for that game's Big Bad. The second game has Hubologists, a cult the player can either join or massacre.
One of the many bits of unimplemented content in Fallout 2 was a quest to procure fuel for their incompetently rebuilt two hundred year old space shuttle which they intended to use to return to their "Sky Father". A fully voiced epilogue for them exists in the game's code, apparently if the player character got them their fuel they would take off shortly after... and find out that they failed to make the hull airtight. Not getting them fuel would result in them concocting a fuel-analogue and blow the shuttle to hell during takeoff. Too bad it wasn't implemented because it'd be pretty damned funny.
Sounds like this idea influenced a quest in Fallout: New Vegas. In this particular quest, you can choose to aid a group of ghouls in their quest to use an old rocket in order to reach space and leave behind the racist human oppressors. Their leader is more or less a cult leader, though he's much nicer and decidedly not psychotic. If you get them the fuel, they take off successfully (unless you deliberately sabotage the launch). Amazingly enough, if their flight goes off without a hitch, the epilogue states that they actually survive and return to Novac in order to help defend it from Caesar's Legion.
In Secret Files: Tunguska, the cult in the game believes that they were descendants from aliens. They are also responsible for your father's kidnapping, but turns out to be the good guys, kidnapping him to protect him from the evil corporation trying to create mind-control machine from the remains of The Tunguska Event and silencing anyone related after they have outlived their usefulness. The sequel has a more traditional doomsday religious cult who's responsible for all those disasters.
Daedric cults in The Elder Scrolls series both play straight and avert the idea of cults being a Religion of Evil. While they aren't worshipping the official religion of The Empire, the belief in the Nine Divines, daedric cults are generally decent or at least halfway decent people and even worshipped quite officially in some places, most notably Morrowind. Daedra do have a tendency towards Blue and Orange Morality though, so they might still do some weird stuff, at least. Despite that, there are quite a few not-so-nice ones too, especially the Mythic Dawn. There are also a few non-daedric cults, such as those weird people in Hackdirt.
The Church of Unitology in Dead Space is a very large, very successful cult by the time the games take place, but it is still a cult. One that seeks to control over an artifact of evil that turns people into necromorphs, and spread it through out humanity.
And then there's the Covenant, where the leaders don't even realize they're running a suicide cult.
The Cultist faction in UFO: Aftershock.
Dr. Wood in Die Anstalt starts one among the patients partway through his therapy. He takes their most precious material possessions from them, and in return gives them little ravens-claw trinkets and goes through a little "faith-healing" routine with them. He never does anything with the items, only taking them to bolster his own percieved self-importance.
The Cult of Kefka from Final Fantasy VI, which was formed after Kefka became a god over the ruined world, and worshipped Kefka for no other reason than possibly fear. Also referred to the Fanatics. They also have a theme song that has ominous chanting.
The first Neverwinter Nights had the "People of the Eye", who worshipped, and were attempting to ressurect, the Creator Race. It's stated a few times that many of the cult's lower-ranking members had only a vague idea of the cult's actual goals, which might explain why they were working to ressurect a race of creatures that despised all warm-blooded races and were planning to kill or make slaves of them the minute they came back.
The Freeware GameCult, obviously, revolves around the protagonist infiltrating one. It's not made clear what they worship, but it seems to involve meditation and the Bible.
Borderlands 2 has the Children of the Firehawk, who worship Lilith as a fire goddess. Lilith herself is mostly ambivalent towards them as they're mainly obsessed with setting themselves on fire but keeps an eye on them in case they do anything particularly bad, such as human sacrifices. Similarly, the Bloodshots have come to worship arms dealer Marcus Kincaid as "The Gunbringer" after he sends them a shipment of complimentary weapons in an attempt to sell to both them and the Crimson Raiders, even erecting a massive six-armed statue of him that spits out guns in exchange for human sacrifices.
Metal Saga has the Gluteus Maximus cult, which is a cult of bodybuilders. You can even join this cult and get one of the bad endings, in which your party comes out with Heroic Builds. It doubles as a Non-Standard Game Over since you also get this scene if you lose any battle while in the church.
In the Grand Theft Auto series, references are made to the Epsilon Program, a Scientology-esque group, mostly in passing on the radio. In Grand Theft Auto V, the Epsilon Program takes a larger role in a series of side-quests for Michael, asking him to perform various tasks in order to advance through the Program's ranks, a lot of which involves paying increasingly higher amounts of money.
MAG ISA — The antagonists are part of a fictional cult known as ''The Order''. Their belief system is a mixture of Christianity and New Age beliefs.
In the Back Story of Last Res0rt, Arikos's crimes stem from leading a cult of Talmi who believed that he could turn them (back) into humans. In truth, Arikos used the cult as a means to produce his Celeste offspring, and not only killed off any "failed" offspring , but also any members of the cult who had outlived their usefulness (specifically older members who could no longer work / bear children) throughout the process.
In Templar Arizona there is a cult of people founded by 'Jake', whose core beliefs revolve around theft, polygamy, and breeding, and refer to themselves as 'Jakes' or 'Jakeskin' (Jake's kin).
The demon K'Z'K has its own cult in Sluggy Freelance, complete with a leader who plays fast and loose with her interpretation of scripture. Very much a Religion of Evil.
A group of cultists shows up on a couple of occassions in direct opposition to the Light Warriors in 8-Bit Theater. It's name is never mentioned as it "cannot be said or written without driving you mad." The cult is a good example of a Religion of Evil and appears to worship beings similar to those found in H. P. Lovecraft's works.
In Our Little Adventure, the group comes across a poster for 'Angelo's Kids', and since Julie wasn't there, Rocky had to explain to the others that 'Angelo's Kids' is both a youth cult and a pyramid scheme.
Timothy/Camellia in But I'm a Cat Person spent a couple of his teenage years in a doomsday cult focused on one of the series' resident Mons.
The world of Drowtales has several groups who are seen in-universe as cults, with the Kyorl'solenurn clan being the largest with the most direct influence on the politics of the world. Originally a more zealous branch of the religion of Sharess, ever since the mainstream religion began it's decline several centuries ago they've grown increasingly isolationist and extreme. On the opposite end are Nether Cults like the group that eventually became the Vloz'ress, which started as a fairly harmless group who kept to themselves but still faced persecution for their beliefs. Once Sene'kha took it over and killed most of the mode moderate members, including the original leader, things went From Bad to Worse.
The Hymn of One in lonelygirl15, which was actually a front for an evil organisation. The Hymn of One also appears in KateModern, which portrays it in a slightly more sympathetic (though still villainous) light.
Marzipan runs a kindergarten program she calls "LURN": "Life-blossoms Undergoing Re-programming Naturally". The "children" (actually dimwitted grown men Homestar, Homsar, and Strong Mad) are referred to as "life-blossoms", the crayons all have politically correct names ("dermal discoveries" instead of "skin flesh", or "blue" instead of "black") and can't color ("so that no one life-blossom outshines the others. That way, they're all special!"), and the grades are renamed things like roots and grass to give an eco-friendly image even though they still map to letter grades in concept. Strong Bad is somewhat incredulous.
Strong Bad: Marzipan, what kinda cult you runnin' here?
Marzipan: Oh, pretty standard.
In the Neopets plot "Spooky Food Eating Contest", during the catacombs phase, you can encounter three kinds of cultists; Evil, Indifferent, and Friendly. Depending on your actions, they can either reward you with an item or curse you, no matter what kind you bump into.
On Family Guy, Meg is drawn into a cult based almost completely on the Heaven's Gate. Although she's got no idea it's a cult. And then there's Peter founding his own, though short-lived (and more benign), cult.
The Movementarians on The Simpsons drew the titular family, and most of Springfield, into a collective based on worshiping a UFO. (They made them eat lima beans, although a diet of low-nutrition gruel was used to break down hard cases. Homer compensated by eating an entire month's supply.)
It turns out the writers based the Movementarians mostly on Scientology. They managed to do this as Nancy Cartwright, a Scientologist, doesn't believe it's a cult. Go figure.
In the episode "Lisa's First Word", Homer mentions that his cousin Francine (originally Frank) joined a cult: "I think his name is Mother Shabubu now."
One episode of Chip 'n Dale Rescue Rangers had Gadget (as part of a 10-Minute Retirement) join the "Cola Cult". It worshiped TV commercials for soda ("Come along, you belong, feel the fizz of Coo Coo Kola!"), and instead of mass suicide, it had the followers give up their worldly possessions, where they were secretly hoarded by the cult's brutish second-in-command. In a mild subversion, the leader fully believed in the commercial's rather upbeat message, though the Cult was still broken up at the end.
Stroker and Hoop were targeted by a cult of "enlightened cannibals", who drug people and surgically remove their vestigial organs for the group's consumption.
Though they did commit mass suicide via poisoned appendixes to ascend to a comet, so not that enlightened.
In Ben 10: Ultimate Alien, the Flamekeepers' Circle is a cult that worships an alien named Dagon, whom they believe uplifted early humanity. The Circle believes that Dagon will return to Earth one day and bequeath more alien technology to humans and transform Earth into a paradise. In the meantime, the Circle promotes the use of alien technology to improve life on Earth via modernization of schools, hospitals, etc. — this aspect of the Circle is what draws in Julie. All in all, a fairly benevolent cult. Too bad Vilgax's One-Winged Angel form looks exactly like Dagon...And when Dagon does return, he transforms everyone on Earth into his Faceless Goons.
Parodied on Recess in the episode "Swing on Thru to the Other Side", where Spinelli develops a cult devoted to following the teachings of Swinger Girl.