"'God?' Where does such a being exist? You should know by now how the 'Ethos' came about... It was an organization created by Solaris aeons ago solely for the purpose of managing ignorant humans. Its doctrines are just deceptions designed to control the masses."
A religion that appears benign, but was carefully designed from the ground up long ago for a nefarious purpose, usually either to force the subjects of a state to behave as its founders would wish, frequently specifically to never attempt to rise in station or do anything but what they're told (popular with constructed state religions), or to empower an evil god or force without anyone realizing that said god or force is in fact evil. The end result is a Villain with Good Publicity. This is a type of Mystery Cult, hidden not through total secrecy but through its misleading image for the laity. This church is widespread in a large country or even the world, and accepted without question — after all, questioning the Path of Inspiration is a heresy punishable by death. Members are sometimes clearly brainwashed from an outside perspective.
Platoadvocates doing this in The Republic.
A specific subtype of Ancient Conspiracy. Distinct from the Corrupt Church in that instead of being a legitimate religion that went bad, the Path of Inspiration is by design rotten to the core. Distinct from the Scam Religion in that the Path's leaders are true believers, not con artists. If the religion is openly evil, it's the Religion of Evil instead. The typical high-ranking member is a Straw Hypocrite. Usually has a Dark Messiah as the figurehead, whose outright evil is part of The Reveal. May overlap with Hollywood Satanism, especially in Conspiracy Theories.
Compare with the Cult. Contrast with the Saintly Church. Often serves as inspiration for Religion Rant Songs by disaffected believers.
Holy Mauser faith in Scrapped Princesswas actually designed by the aliens who conquered Earth and exiled brainwashed human survivors to a small portion of its surface. Its function was to a) prevent humanity from ever discovering their true history, b) allow semi-sentient weapons named Peacemakers to act without interference as "Lord Mauser's angels", c) rally the entire world population against the person carrying the genetic anomaly enabling her to "cancel" Peacemakers' presence and challenge the status quo, who just happens to be the protagonist of the show. It may be also notable that all this was apparently organized for humanity's own good, at least, from the alien point of view.
Father Cornello's cult the Church of Leto in Fullmetal Alchemist which was created so that Father Cornello could have his own army, Cornello is revealed to be a fraud and is killed, but Envy reappears as Cornello to complete the work using the weak-willed members of the church. There's also the fact that the deity Leto turns out to have been the Big Bad Father in disguise, so the entire religion is an example of this.
Cowboy Bebop's episode "Brain Scratch" had a cult that brainwashed people into giving up their physical forms for a supposed digital existence by recording their brain waves onto the internet.
A most terrifying example is the Holy See in Berserk, who do not even know that the four "angels" they worship and their Messianic Archetype are actually the five members of the Godhand, Eldritch Abominations who each crossed the Moral Event Horizon by sacrificing a whole load of people each (and who knows what else) and are subservient to a God of Evil. Oh, and they torture people. They are CRAZY obsessed with torturing people, often for no reason at all. It is implied that the four angels were originally inspired, not by the God Hand, but by the Four Elemental Kings revered by the pagan religion that the See supplanted, making it a combination between this trope and Corrupt Church.
The Earth Cult in Legend of Galactic Heroes encouraged people to return back to their roots, i.e., the planet Earth, which by the time period of the seriesnote during the late 36th century AD had became an isolated backwater planet. As the series progresses, it became increasingly clear that the Earth Cult's real objectives were to regain the lost status and power that Earth enjoyed centuries ago and would resort to any means, from brainwashing its members to plotting assassinations of key figures in the galaxy, so as to achieve their objectives.
In the world of Ravnica in Magic: The Gathering, the Black/White Orzhov guild are known as the "Church of Deals" and built a religion in order to exploit their faithful and provide a support structure for their inner circle. For example, from the flavor text of Conjurer's Ban:
Orzhov faithful file past to have their minds purged of "impure" desires. There, the guiltwardens eliminate any thoughts of hope or self-sufficiency.
Marvel Comics - The Universal Church of Truth in the 20th century is a galaxy-spanning empire that preaches the message "Convert or Die". It was founded by a time-traveling super-villain for his own evil ends. But in the 30th century on many worlds it has become a somewhat more benevolent and spiritual organization.
The Church of Transcendence in The Authority: its leader, John Clay, infected all of his devotees with a psychic virus. This virus forced them to venerate him as well as give him some of their energy, turning him into a superhuman capable of taking on the entire Authority by himself.
In the movie Logan's Run, everyone lives a hedonistic lifestyle, but are told that when they hit the age of thirty, they must undergo the ritual known as "Carrousel," where they are vaporized with the promise of being "Renewed." This was later discovered to be a lie designed by the computer running things in order to control the population and prevent it from becoming too large. After the film, there was also a TV series.
While Logan's Run was a book before becoming a movie, the book did not have Carrousel.
The Mist had a version of this, in that it was one woman's interpretation of religion that inspired the people in the store to form a cult and attempt human sacrifice
The James Bond film Licence to Kill had TV evangelist Professor Joe Butcher and his Olimpatec Meditation Institute serving as a front for Franz Sanchez's drug empire, with their donations going toward Sanchez's operations and "targets" being drug dealer lingo for agreeing new market prices for their product.
In Edgar Rice Burroughs's John Carter of Mars novels, the religion of the red Martians, which encourages the old and infirm to make a pilgrimage to the South Pole in search of heaven, was created and is controlled by a society of cannibals who use the pilgrims as their primary food source. Their religion is in turn the product of another sect of cannibals who feed on them. When John Carter discovers these facts, and relates them to the world at large, he's nearly executed for heresy before he manages to prove it.
In Isaac Asimov's Foundation provides a rare example of this trope used for what are unquestionably good aims. The titular Foundation manages to turn the four empires surrounding their homeworld, Terminus, into puppet states by creating a "religion of science" as a guise for providing technological aid while gaining influence. At one point, despite handing the Big Bad of one story a battleship to invade Terminus with, the Foundation proved that it had ultimate control of both the technology and the people. The result is that the Foundation is preserved and expands its influence—a key part of Hari Seldon's Plan to cut the Galaxy's dark age from 30,000 years to a mere 1,000.
Showing off his abilities to understand the changes in societies, in a later book of the series, someone attempts to use that religion and finds out that economics is now more important to the current people than religion. The time of religious fervor has passed.
The Clave from the Second Chronicles of Thomas Covenant commits mass human sacrifices "for a good cause". Unfortunately, it doesn't quite work like that...
The eponymous Electric Church of Jeff Somers's cyberpunk novel "The Electric Church". Adherents of the faith have their brains mounted in artificial bodies to give them "time enough" to discover the truth of salvation. They tell others that "Time is your enemy" and ask them to "Let us show you an endless trail of sunsets," offering free immortality to anyone and everyone. Systems in the artificial body suppress your higher brain functions to keep you an obedient servant. The whole thing is a monstrous world-conquering scheme to rule by religion, facilitated by the fact that converts keep their legal status as citizens in the world government because the brain is still alive, despite all free will and volition being suppressed by the technology involved.
In an alternate future to the Expanded Universe of Star Trek: Deep Space Nine, a large number of people in the "Bajoran Ascendancy" worship the True Prophets in the True Celestial Temple, a second wormhole that leads to the Grigari Meld in the Delta Quadrant. Most of these people are brainwashed by the Grigari, but the Grigari themselves are true believers—because the True Prophets want to reduce the universe to a mathematical abstraction.
The Bene Gesserit of the Dune-iverse. Specifically the Missionaria Protectiva, the subgroup which spreads the set of beliefs called the Panoplia Prophetica.
Subverted when the major prophecy spread by the Missionaria on Arrakis ends up being fulfilled by Paul-Muad'Dib, much to the surprise of the Bene Gesserit.
Subverted again by Leto II, this time intentionally. After merging with a sandworm, he sets himself up as God Emperor of his own theocratic state, with the state religion specifically designed to be as restrictive and frustrating as possible for humanity. That in turn is part of his plan(Thanatos Gambit, actually) to get humanity to save itself through expansion and innovation, making him a Necessarily Evil form of this.
In the Animorphs books, The Sharing is a Path of Inspiration that is disguised as a secular fraternal organization. It provides fun, social occasions, and volunteer work for the community, but its real purpose is to seduce people into voluntarily allowing themselves to be taken over by alien invaders called the Yeerks, and to serve as a front organization that keeps up the Masquerade.
In Lord of Light, Hinduism is used for this purpose, to allow a handful of self-styled gods to control all technology under the guise of protecting the populace from progress too quick for them to understand. The protagonist uses Buddhism as a religious tool to recruit the opposition. It is worth noting that said protagonist only picked Buddhism because he needed to represent a religious leader as a way to present change as an option; when asked "why Buddhism?" he replied that Christianity would have hurt.
In Neal Stephenson's Snow Crash, L. Bob Rife's religion is in fact an attempt to render people suceptible to brainwashing using the ancient Sumerian language, which is in fact a programming language for the human brain. The title refers to the drug that does this, and the computer virus that can do this to people in the virtual world
If it's possible to have a secular one of these, the Brotherhood in Invisible Man is this in spades. Even the lower-ranking officials don't realize just how much the organization focuses on gaining power, and how little its highest-ranking members really care about helping the poor and downtrodden.
Kokchu, the shaman in the Conqueror books, uses trickery and sleight of hand to make it seem as if he is performing miracles and thus exert religious influence over the Mongol nation. It's somewhat ambiguous to what extent he himself believes in his own teachings.
David Weber's Safehold books feature the Church of God Awaiting. It was designed by megalomaniac Luddites gone mad with power to prevent the last colony of humans from ever redeveloping advanced tech, in an attempt to avoid the attentions of the xenophobic alien Gbaba. And, of course, to feed the egos of the megalomaniacs in question by making them into "Archangels." The original idea for the colony was that they would abandon advanced tech for a few centuries to hide from the Gbaba, but preserve records of tech and the existence of the Gbaba so that the colony would know what to avoid doing until they had tech advanced enough to destroy the Gbaba. In the eight centuries between then and the present day, the members of the Church of God Awaiting, ignorant of this, also make it into a Corrupt Church.
In the Han Solo trilogy of the Star Wars Expanded Universe the T'landa T'il can produce a state of complete pleasure in a person. This state of pleasure is highly addictive. Normally it is used to attract T'landa T'il females, but instead the self appointed priest use it to lure their victims to Ylesia. They go from planet to planet and recruit people. People who experience it and are not strong enough to resist it are drawn into it and become addicted. The pilgrims become slaves in the Ylesian spicemines. The revival is a major part of their day where the pilgrims get their daily fix. These poor slaves are completely brainwashed and can not live without their drug. The faux religion that the T'landa T'il have established is just a ploy to get free slaves and spice. The whole operation is owned by the Hutts. When the slaves are brainwashed and dependent enough they get shipped off to the spice mines of Kessel or sold as sex slaves in a brothel.
Speaking of Star Wars, the Potentium Heresy. It says that dividing the Force into good and evil is too simplistic, and that as long as you listen to the Force, everything will work out for the best. It was a Sith lie. It actually catches Han and Leia's son, though he, somewhat Genre Savvy, doesn't teach Luke's son about it. This leads to a huge What an Idiot moment.
The Chapter from Book of the Long Sun probably qualifies, because although individual members may be kindly or even saintly, the gods that they worship are in fact the uploaded personalities of a dictator, his family and some of his closest advisers, almost all of whose idea of a commandment is Your government isn't sacrificing to me enough; overthrow them right now and let me know when you've done it; if you sacrifice enough children to me you'll probably get my attention.
The Lazarus Intent in the Doctor Who Missing Adventures novel The Crystal Bucephalus was set up by a criminal who ripped off Christanity wholesale to create a religion which, rather than teaching the Messiah was resurrected and would return, taught that it was up to believers to invent time travel, and rescue their saviour from the moment of his death. The Doctor notes that while the church may be a fraud set up by a egomaniac (Lazarus isn't even a Dark Messiah, just a conman who thinks big), devout Lazarites tend to be good people.
Nine Princes in Amber has a variant on this where the Amberites can walk in shadow to find a planet where they've already been worshipped as gods, so that they can recruit the population as fanatical legions of foot soldiers.
In The Chronicles of Narnia, the Calormenes worship their god Tash, who is definitely a real and evil demon. Tash's cult has plenty of the trappings of being Obviously Evil; so far, it superficially appears to be a Religion of Evil. But we eventually meet a man named Emeth who is pure of heart and attained entrance to Heaven—who nevertheless was a pious member of Tash's religion—thus proving that the Calormenes (who are just normal humans, after all) are mostly just deceived and exploited, and not the kind of evil persons who would join the Religion of Evil.
The religion started by Shift and Puzzle definitely counts. Originally, Shift is just deceiving creatures into believing Puzzle is Aslan so he can get whatever he wants. Then things escalate and he teams up with some equally opportunistic Calormenes to create the worship of "Tashlan", a mash-up of Aslan and Tash that true believers of both are equally horrified at, so that he can get rich selling Narnian resources (including its people) to Calormen.
C.S. Lewis caught considerable flak for writing "The Last Battle," including accusations of being racist, with the claim that the Calomene's were thinly veiled parodies of Arabs. C.S. Lewis's real point has nothing to do with race at all. Rather, the "Tashlan" bit seems to be a Take That against religious syncretism as a means of forming a super-religion.
The syncretic mishmash of world religions called Enigma Babylon One World Faith that becomes the official one-world religion during the first half of the Tribulation period in the Left Behind books, believing that all religions are true and have valid paths leading to God, yet denouncing biblical Christianity (as defined by the books' authors and the Tribulation Force characters) and its message of Jesus Christ being the only true way to God as heretical. In following with the interpretation of Mystery Babylon in Revelation chapter 17, this "anti-church" was merely set up to serve the Antichrist for a time and then would be destroyed, only to be replaced by the single-deity worshipping religion of Carpathianism.
In Charles Stross's The Apocalypse Codex Bob Schiller's Golden Promise Ministry appears to be another American fundamentalist Christian sect, with maybe a few odd doctrines. This being a book in the Laundry series, Schiller and his inner circle actually serve a powerful Eldritch Abomination, not entirely willingly. Once Schiller completes a human sacrifice of nearly unprecedented scale the entity will escape its prison under alien stars, and humanity will end. It's a comedy.
Renewalist Church, official religion from Midnight World. Basically, it's Christianity, but bowdlerised so hard that it's not dangerous for the world-ruling vampires.
Live Action TV
The Divine Order in Lexx is a textbook example of this trope.
Stargate SG-1: "Hallowed are the Ori". Interestingly, after the Ori are killed, in The Ark of Truth, their former subjects take up Origin as a legitimate religion, albeit with some changes. "Can you take out the parts about burning people alive?"
The series implies in the final season that Origin is a largely benign religion, possibly one followed by some Ancients before their Ascension. The Ori are corrupting it and using it as a tool to control their followers, some of whom realize this and are extremely angry, but are largely powerless against the Ori and their Priors.
Daniel Jackson, having read the Book of Origin, from time to time quoted passages that seem to contradict the Ori forces' actions. This never worked. Likewise, Ori worshipper Tomin calls a Prior out on his twisting of Origin, signalling the start of his Mook-Face Turn.
We also see snippets of the Goa'uld religions that suggest they're trying for the Path of Inspiration vibe, but due to the Large HamChaotic Stupid nature of the Goa'uld, they mostly come across as straight-out Religion of Evil (a large portion of the Jaffa population was loyal more out of fear of getting their brains melted rather than any genuine spiritual devotion).
In the third season of Weeds, a new suburb called Majestic which ultimately absorbs Agrestic in a kind of weird symbiosis springs up next door. The community is centered around Absolute Truth Ministries, an ecumenical, quasi-Christian megachurch which exists to propagate a religious conservative ideology and fleece its congregation and the community for everything it can get (the massive sign on the complex not-so-subtley highlights its acronymn, ATM).
The Trope Namer is the state religion of Riedra, created by the Quori forces of the Dreaming Dark in the Dungeons & DragonsDungeon Punk setting Eberron, because it both oppresses the masses and helps empower a great evil. The books go out of their way to stress that life under the Path of Inspiration is not bad at all: its followers lead a life of relative peace and sanctity. The only major point of contention from the point-of-view of an informed outsider is the whole "tricking followers into helping empower a great evil" bit.
The Blood of Vol from the same setting is a lesser example. To the common man, it is a slightly creepy but otherwise okay religion that views blood as a gateway to immortality, and venerates undeath as a great martyrdom for the sake of teaching others ( as in Eberron, undead creatures are not Always Chaotic Evil). Considering that the afterlife of Eberron consists of a drab wasteland that slowly erases your memories until you're a mindless wandering shade, you can see where they're coming from. The truth is a little harsher: The Blood of Vol is actually being manipulated by Big Bad Erandis Vol in order to advance her agenda in Khorvaire, with the actual dogma being an altered form of House Vol's beliefs preserved by elves fleeing Aerenal.
The Eternal Order and the Church of Zhakata in the Ravenloft setting.
Okay. Follow this closely. Deadlands has more Cults than you can shake a jackalope's foot at, and at least a few of them masquerade as legitimate religions. Then there's the most visible example and/or subversion, the Church of Lost Angels. Beginning as a standard Protestant sect, many people suspect the Lost Angels' leadership to at least be involved in power grabs centering on the scarcity of food near the eponymous City of Lost Angels. (It's amazing how much someone listens when you're giving them the only hot meal they'll have all week.) Then there's The Reveal: the "hot meal" is made of people, and their raison d'etre is the corruption of the unsuspecting. Two centuries later, though, the Angels are most definitely on the side of, erm, angels. Subversion? Inversion? Double Subversion? You decide!
Most chaos cults in Warhammer and Warhammer 40,000 appear to be legitimate on the surface and both settings have a lot of people who are worshipping or aiding the Ruinous Powers without being aware of it. For those in the inner circles, however, it's plain Religion of Evil.
The Universal Brotherhood from the Shadowrun game did this. The nice benevolent facade hid a collection of bizarre alien insect-beings whose main purpose was to infuse insect spirits into its members. An orbital nuclear strike was avoided only because said nuke was delivered at ground level, unleashing horrible horrors into Chicago. And that was the good ending of this saga.
Hunter: The Vigil features The Knights of Saint George, ostensibly a secret society within the Anglican Church devoted to battling sorcerers because they believe magic primes the world for invasion by "dragons." As the members climb the ranks in the order, however, they slowly learn that the "angel" they supposedly gain their power from is actually a fragment of the Abyss, a rift in the basic concept of reality.
In Mage: The Awakening the Seers of the Throne Ministry of Paternoster is devoted to making every religious faith as dogmatic and closed-minded (especially in regards to magic) as possible, in accordance with the commandments of the Exarchs. Notably, they don't want sleepers to directly worship the Exarchs, since they believe that for anyone other than a mage to do so profanes them.
They also believe their own hype. All of it. They even have their own priests and ceremonies!
And if you belong to certain Orders, you can actually run your own benevolent version. The Guardians of the Veil maintain Labyrinths, fake conspiracies and occult practices meant to groom worthy individuals into Awakening and shunt those not up to the responsibility into a tiny pocket of lesser occult knowledge. The Silver Ladder, meanwhile, runs Cryptopolies, mixtures between civic organizations and mystery cults (think Freemasonry) that are meant to teach Sleepers the lesser principles of Awakened wisdom before they come into the greater ones.
Every new cult or religious sect that gets a mention in Cthulhu Tech is actually just a front to indoctrinate the vulnerable into cults worshipping evil horrors from beyond. But the game has "Cthulhu" in the title, so what did you expect?
The Immaculate Order in Exalted qualifies as this. Instructing the masses never to attempt rising above their station impedes the development of exemplariness necessary for Celestial Exaltation. Furthermore, if any of them do reach those lofty heights, the faith has spent centuries spreading the belief that they are Anathema, normal humans overwhelmingly and irrevocably possessed by demonic intelligences. Considering that the Solar Exalted went nuts and unknowingly threatened to bring the world to ruin, keeping more of them from showing up doesn't seem like an entirely bad idea...
This, combined with the the fact that it actually does tend to lead to a nice, happy community if followed correctly makes it actually a bit closer to the version in Plato's Republic — a religion deliberately founded for the good of the people. Whether or not they actually succeeded is, as with many Exalted morality issues, a matter of debate.
To provide a bit of black to the debate, we have the state religion of Skullstone, which was created entirely to produce a regular supply of soulsteel for the Silver Prince's ersatz First Age fleet.
The Path of Inspiration of Eberron is seen, by name, in several high-level adventures in the Dungeons & Dragons Online game. Player characters with the True Seeing ability will see the not-so-diminutive Quori creatures, which animate and control the faithful, latched on the head of the Inspired. They preach out in the streets about their happy ol' church, with none (but the player characters) ever the wiser.
Brotherhood of Nod! They're usually depicted as a quasi-cult with their leader, Kane, determined to continue the spread of the ecology-destroying Tiberium substance with the belief it would advance the human race. It's even more so in the third installment of the Tiberium series on a massively successful scale, getting a large chunk of 80% human population who live in the deserted Yellow Zones to go against GDI and work on his goals even further.
Then subverted in the final installment as in some case, they were actually right.
The Glabados Church from Final Fantasy Tactics qualifies, though one must both play through the whole game and read the Germonik Scriptures to get this whole picture.
It also seems that even among the highest officials of the Church, few know of its true origin and purpose. Simon, for example, rose to become one of Church's most powerful priests, before accidentally discovering the Germonik Scriptures and learning the truth. Though many of those who aren't aware are rather evil anyway. Thus, Glabados could be seen as both a Path of Inspirationand a Corrupt Church.
The religion of the Urkan from Breath of Fire III also somewhat qualifies. Though their god isn't exactly malevolent (just so overprotective of the world that she decided to commit genocide on a race that COULD destroy it, even though they were a very peaceful race), she IS the final boss.
The Church of Yevon from Final Fantasy X was created to make people accept the periodic resurgence of Sin (unbeknown to most, a creation of the summoner Yu-Yevon), formalize the stopgap means used to keep him at bay, point the masses at a scapegoat, and as a result prevented anyone else from coming up with a permanent method of destroying Sin. Though they believed that there simply WASN'T a means to permanently defeat him.
The Fellowship from Ultima VII are rather obvious about this, having been created by the Guardian for the purpose of subverting the virtues and turning the Britannian people against Lord British and the Avatar.
The Divine Ascension in Pandora First Contact is a religion based on social networking, used to collect data and blackmail their followers, at least that's how it started out.
The Church of Martel from Tales of Symphonia is a worldwide scam created by the Big Bad Yggdrassil to keep the mana flux between worlds passing through the Tower of Salvation, and to have a reason to choose "Chosen Ones" that will give themselves up of their own free will. These things are used in his attempt to revive his sister, Martel.
Tales of the Tempest looks like it'll be this, but the church is actually good, and the pope was being manipulated.
The White Mantle in Guild Wars straddles this and Corrupt Church. The founder of the White Mantle was a decent guy who wasn't aware the Mursaat were evil; by time that became apparent, the Mursaat had saved his people and taken him away never to be seen again. On top of this, once the Mursaat are beaten, it turns out they had been holding back an even worse evil.
The Cult of the Watchers seems to be the state religion of The Empire in Drakengard, though actually they don't even bother making pretenses of good intentions. They just straight-up Mind Control all their subjects and anyone they capture. It's the quicker, easier way really. It's not a Religion of Evil because the "Watchers" they serve and worship are the same beings as the gods worshiped by the Crystal Dragon Jesus religion.
The Records of Fate (the Save Points in Chrono Cross) were set up as a way for the residents of the El Nido archipelago to not only record what they did, but also get any information they need. Naturally, this is all a part of the supercomputer FATE's plan to keep the people of El Nido (and YOU) in that area and never wander into the rest of the world that Chrono Trigger took place in.
In World of Warcraft, the Scarlet Crusade appears like this to Alliance players in a major quest line leading up their instance. Then after this quest line has shown that they are a Corrupt Church, players encounter another turn of events in Stratholme, a high level instance, where it turns out that the faction was led by a demon.
In the Halo series the Covenant is both a religion and an interstellar alliance incorporating multiple species. They worship the Forerunners, who they think Ascended to a Higher Plane of Existence by means of the Sacred Rings, and seek to recreate this "Great Journey." Unfortunately for them, what actually happened was that the Forerunners lost their war against The Virus and decided to go out by annihilating all sentient life in the galaxy. In the second game, the Prophet of Truth seems to be redirecting the Covenant into a Corrupt Church, eliminating his fellow prophets and concealing key facts from the wider Covenant.
A relatively recent development in Covenant history, detailed in one of the Novelizations (Contact Harvest?), also puts them in Corrupt Church territory. Upon discovering humanity, Forerunner computers used by the Covenant identified them as "Reclaimers," one of the holiest terms in the Covenant religion. This invalidates much of the Covenant dogma, so the 3 prophets decide to cover it up by assuming power and Kill All Humans.
The Circle of Thorns in City of Heroes are part this, part Ancient Conspiracy, and... well, they kidnap random people and have them possessed by ancient ghosts, and that's just the start...
The Order of the One True Way from Suikoden Tierkreis believe in predestination to ridiculous levels, to the point of not running in terror when a townsperson is struck and killed by lightning because their leader said it would happen.
Dead Space features the Unitologists...and their Marker, which unleashed a horde of zombies when the Unitologists began not only studying it, but worshipping it (and the guy who found it). More generally, they're aiming for an Assimilation Plot—but interestingly, they don't keep that part a secret. They just don't tell people that the assimilation involves getting murdered by bloodthirsty zombies and bonded to an undead necromantic Hive Mind.
Grandia II: You know that war that happened 10,000 years ago between Granas, the benevolent creator, and Valmar, the destroyer? And how Granas won? That was a bit of a lie. The truth is... when they both defeated each other, Granas was the one who died and Valmar was split into multiple pieces. And the highest members of church knew this and kept it from the general populace, to keep order. Furthermore, Granas and Valmar were never truly divine in the first place. They were merely scientists who unlocked the power to warp reality and used it to set themselves up as gods.
The Diablo lore, expounded in tie-in novels, has two significant cases: the Triune, an apparently benevolent church that was actually a front for the machinations of the three Prime Evils. Much later, the Black Road did much the same thing, but it was a more obvious deal-with-the-devil situation.
Averted and lampshaded at the same time by Adventurers! In this strip, a character mentions a church, which instantly worries Karn, until she specifically assures him that it's not a front for an evil mind-controlling organization.
The Way in Juathuur. It actually ensures that juathuur will not achieve power over men.
The spirit's cult in The Phoenix Requiem didn't start as one, but became one once its origins were forgotten.
The basic shtick of the Luminositan Church in Errant Story, founded on a Deity of Human Origin which its priests use to keep the country of Veracia under their thumbs. (In fairness, it was the magical energy pumped into Luminosita that had much to do with Veracia becoming a world power to begin with, and we're not sure yet that Luminosita is of human origin, but he certainly isn't one of the "real" gods of the Errant World.)
The Hymn of One in lonelygirl15, a front for the sinister Order of Denderah.
The Hymn of One is central to the plot of KateModern.
From the Global Guardians PBEM Universe, the Society of Human Fulfillment is a Scientology-like cult that masquerades as a nationwide chain of self-help clinics. It's actual agenda is to stir-up anti-metahuman sentiment through very subtle brainwashing techniques.
The Fifthist Church in SCP Foundation materials is a textbook example. On the outside, it's a harmless celebrity cult with a Secret-esque self-help book as its centerpiece. When given free reign, they very nearly destroyed the world.