Many of the towns that Kino visits in Kino's Journey have a dark secret somewhere along the line. Sometimes it isn't an actual secret, but just something that casual travelers won't notice at the first sight, while at other times it's played dead straight.
The town that Kirika wanders into in Noir was founded for the sole purpose of guarding the entrance to Altena's manor, and the villagers will kill anyone who interferes with their instructions.
Kur˘zu-cho from Uzumaki seems normal enough... for about five minutes. Then people start going insane, turning into giant snails, whirlpools start sinking any boats that come near... you know, all the normal risks of building your town on top of some kind of crazy Cosmic Horror Story spiral shrine that is both alive and seems to just really, really hate people. All people. A lot.
In Monster one of the towns mentioned was used for child psychological experiments.
In the "Dressrosa" arc of One Piece, the port town of Acacia appears to be peaceful and pleasant, despite being ruled by Doflamingo; a place where people and toys live together, and gladiators fight in the colosseum. But the Straw Hats soon find out that the numerous living toys on the island are actually humans changed by a Devil Fruit user, and all memories of the transformed humans are erased aside from those of the toys themselves. Those who lose in the colosseum are fated to become toys...some of which are prisoners for rebelling against the Donquixote family. Oh, and also, Doflamingo is only in charge because he framed the last ruling family and won the public's heart with Engineered Heroics.
One Piece's sixth movie has an island with a dark secret.
We also have Water 7. On the surface, it seems like a happy, Venice-like city where its premier ship-building company makes ships for people all over the world, and they have a railroad that runs on the ocean. We later learn that island it's on is sinking, not helped by a Giant Wall of Watery Doom that hits once a year, and the president of said ship-builders holds the blueprints for a world-destroying battleship, currently being set up for an assassination from the Government.
Even Luffy's home island has this; the Goa Kingdom seems like a perfect and beautiful place...but only because the kingdoms rulers throw everything that would make it look bad, people included, into a giant landfill that has become a district unto itself. And when some World Nobles are scheduled to visit, the rulers decide to have everything, people included,burned to the ground.
Wildstorm's comic book sequel to The Texas Chainsaw Massacre (2003) remake reveals that the residents of the town are completely aware of Leatherface and his family's murderous and cannibalistic tendencies, but don't do anything out of fear of retribution. At one point, after the heroine escapes from the Hewitt family lair and makes it into a bar in town the patrons stop her from calling for help and bring her to the pursuing Leatherface.
Bar Patron: "We don't want no Hewitt trouble."
While we're on the topic of Wildstorm, this is essentially the entire premise of Out There. El Dorado, California is a prosperous community — because of a Deal with the Devil. Four local teenagers find out. Hilarity, as you can imagine, ensues.
Matt Murdock finds himself run afoul of one of these in Daredevil: Reborn — there's an old quarry filled with corpses, and he almost gets added to the pile after the sheriff discovers who he is.
Nightwing once encountered a town where every inhabitant was in the witness protection program, and the inhabitants where prepared to kill to ensure that no one from their old lives find out where they were.
The Fantastic Four, at the beginning of their superhero career defeated a group of Skrull spies. Reed Richards brainwashed them into becoming cows and retaining that form for life. The milk from these cows affected a small dairy town named King's Crossing, causing the inhabitants to develop shapeshifting powers and become paranoid and insular. The Fantastic Four, via a girl Johnny Storm was dating, ended up investigating the town and neutralizing the threat.
According to Runaways, the reason that the Los Angeles of the Marvel Universe isn't crawling with supervillains in the same manner as New York City is because for years all the criminal activity in L.A. was controlled by the Pride, who were so evil and vicious that no sane criminal or supervillain dared to cross them.
In the Firefly fanfic Forward, the unnamed village in the "Charity" story is being attacked by mercenaries/slavers for unspecified reasons. As the story progresses, things become a lot clearer. The village had been infiltrated by an "Inducer" psychic, who could control people's emotions. Being a product of the Academy, she is less than stable. The Blue Sun corporation tracked her down after she murdered an entire Blue Sun facility using mind-controlled villagers, and sent the mercenaries to recapture her.
In Toy Story 3, Woody and the gang wind up in a day care that looks like paradise. The toys (led by a fluffy stuffed animal named Lotso Huggin Bear) are all friendly, there are always lots of kids to play with them so that none of the toys ever get outgrown, and there's a repair ward that keeps the playthings in tiptop shape. However, their dark secret is that, in order to stay in the older kids' playroom, the ruling toys regularly sacrifice new toys to the toddler's playroom, where too-young children bash and beat toys until they are destroyed and thrown out.
Atlantis II: Milo's Return has an effectively creepy and chilling version of this which could come straight out of Lovecraft Country: the first tale in the arc consists of a constantly foggy, frigid Norwegian town where all the townsfolk seem to be hypnotized, brainwashed, or under a spell. If the constantly bulging eyes, monotonous voices, and deathly pale skin doesn't scare you enough, the so-called leader of the town is secretly in league with a Kraken, linked to it through some form of telepathic connection which grants him eternal life and power, as long as he continues to sacrifice hapless travelers to his master/slave. (The...relationship is never quite pinned down as to who really controls whom.) And in what may be a clear homage to, or at least an echo, of Shadow over Innsmouth, after the villain and the Kraken are eliminated and peace, sunshine, and happiness return to the townsfolk, a deleted alternate ending shows the innkeeper with her baby...which extends a Chthulu-like tentacle out of its blanket to caress her cheek, while she lovingly coos and starts talking about it 'growing up big and strong'. Whether this implies Face Full of Alien Wing-Wong or simple Body Horror is up to the viewer to decide.
Films — Live-Action
The 1955 film Bad Day at Black Rock is one of the codifiers of this trope. It concerns a veteran of World War II heading to the town of Black Rock to pay a visit to Komoko, the father of a Japanese war buddy who died trying to save his life, only to find that the entire town has something to hide — namely, that Komoko was murdered by Reno Smith, the most powerful man in town, a racist landowner who tried to cheat Komoko by selling him some arid farmland with no water only for Komoko to make the farm prosperous by digging a sixty-foot-deep well. Soon after Pearl Harbor went down, Smith got drunk with a handful of others, harassed Komoko, burned his farmstead down and shot him.
The Stepford Wives concerns a small community where every woman acts like the perfect wife. Only it turns out that the "wives" are actually robots who are programmed to act this way, and they are replacements for the real wives of Stepford who are murdered by their husbands.
Hollowed Ground is about a small farming town who kills visiting families and tries to make one visitor give birth to their messiah.
Beautifully subverted in the movie Big Fish with the mysterious town of Specter: the idyllic small town exuding a weird feeling of wrongness appears to be a textbook version of this trope (complete with hints that no one ever leaves, a woman with a Stepford Smiler-esque grin, and all its residents inexplicably going barefoot all the time), but The Reveal never comes; it's simply a Quirky Town.
It's never explicitly stated, but Specter is supposed to be heaven. No-one leaves, everything is perfect, and there's the talk and surprise of people stumbling in before their time.
There's also the fact that the version of Specter we see in the film isn't quite the real thing- Ed Bloom is exaggerating the story. It's more likely he found a very nice, idyllic town as a young man, but simply felt like he didn't fit in, or that he deserved more challenge in his life so he left. Everyone being barefoot and that business about expecting his arrival might've been minor occurrences he blew out of the water or simply made up entirely. No Reveal was made about the town's secret because there wasn't one.
In the movie Hot Fuzz, all the members of the town of Sandford's Neighborhood Watch secretly murder everyone in the town that is "unpleasant", so that nothing stands in their way of winning "Village of the Year". All murders are disguised (sometimes poorly) as accidents.
The John Carpenter film In the Mouth of Madness features the surreal, warped town of Hobb's End, which may or may not be the fictional creation of horror writer Sutter Cane. Features of the town change and rearrange themselves, the residents are monsters in disguise, and the Last Sane Man ends up taking shelter in a movie theater where the events of the film are playing out on the screen, as the world burns down around him.
Implied in the Friday the 13th (2009) remake, where at least one resident was shown to be aware of Jason living and killing in the old campgrounds. This is markedly different from the originals, where the residents of Crystal Lake didn't seem to know exactly what was going on at the camp, but were pretty clear in their warnings to outsiders.
In Freddy vs. Jason, many adults in Springwood know of Freddy's dream-killings, but have conspired to conceal this from the town's youth to starve him of the fear that gives him power over dreams. Jason comes to Elm Street at Freddy's instigation, so his killings will revive old stories about the Springwood Slasher and restore Freddy's powers.
The nameless village in the middle of the swamp in Sauna. Their dark secret is the titular sauna, and they would be really glad if no-one ever came in or paid attention to it. They're not bad people in any sense, more like reluctant guardians of an evil secret the world is better not knowing.
In Dagon, based loosely on H.P. Lovecraft's The Shadow Over Innsmouth, the people of Spain will not speak of or visit Imboca for good reason: the city was taken over by an pagan god when its desperate people turned to him for help.
In Eye Of The Devil David Niven (as a French count) must return to his home to be sacrificed for a better crop or something. The entire town are Satanists posing as Catholics, including their priest
Inverted in Purgatory. All the townsfolk of Refuge are Famed in Story dead outlaws, murderers, or prostitutes who must live virtuously - no violence despite abundant weapons, little swearing, no theft despite the well-stocked general store, no drinking despite the saloon - for ten years before they can go to Heaven; one wrong move and they're taken right to Hell. Living people can sometimes reach the town, so all of its residents take a Meaningful Rename and perform a Masquerade of simplicity and normalcy for them, hoping to be left alone to serve their sentences. It's a dark secret for them, because they believe they have to either let themselves be killed or go to Hell if they fight visitors, but harmless enough to keep - they're even willing to let someone more peaceable who finds out leave.
Winter's Bone: Everyone is connected in some way with the meth business, and just about everyone knows who killed the main character's father.
The whole unnamed town in the horror anthology film Terror Tract is fucking nuts!!. Consisting of nothing but strange deaths, and bizarre incidents that a realtor tries to hide from a couple who wants to buy a house in the area....except he can't keep the secret and tells the buyers about each house's sordid grisly background.
The Truman Show. In this case, everyone's in on the secret except one of the residents...
Author Stephen King calls this "The Peculiar Little Town" and has confessed that he has a weakness for writing stories of this type (among them Children of the Corn, Rainy Season and You Know They Got A Hell Of A Band).
His best known peculiar little towns are Derry (IT) and Castle Rock (good number of stories), both in Maine, which tend to redline the weird-shit-o-meter on a regular basis. In the end, Castle Rock is destroyed, which is probably for the best. Castle Rock is destroyed by a visiting evil that took advantage of the secrets and flaws of many of the townspeople so that it could take their souls.
Haven — which is near Derry, in The Tommyknockers. It starts off as a normal town, but becomes this trope when the alien spaceship is first unearthed and slowly makes everyone crazy and obsessed with it.
The town Jerusalem's Lot from 'Salem's Lot. It's had a family of gangsters that worships demons and consorts with vampires. One of these vampires comes to town and then it really has a dark secret. By the end, the whole town is undead except for the protagonists who burn the town down and leave. A couple of later short stories by King reveal that burning down the town only temporarily halted the vampires. And it's hinted throughout both the novel and the prequel story that we still don't know the worst of its secrets.
The townsfolk in Rainy Seasontry to warn people about their annual "bad weather problem," because warning the newcomers is part of the tradition. As is the inevitable death of the newcomers — always a young man and woman.
The residents of Ludlow, Maine keep the secret of the realPet Sematary, the Wendigo, and what lies beyond the deadfall...
The eponymous town in H.P. Lovecraft's short story The Shadow Over Innsmouth is a decaying seaside town where everyone has the distinctive "Innsmouth look". Eventually the narrator discovers that the residents are half-man / half-fish and worship the Deep Ones.
Kingsport in "The Festival". Or, rather, the "dream version" of Kingsport. The "dream version" can't have been entirely imaginary though, since in the later Lovecraft story, "The Silver Key" the protagonist is casually mentioned to have read about excavations under Kingsport's church that revealed a hidden system of tunnels mentioned in "The Festival".
Possibly every town in Lovecraft's imaginary New England. Naturally, the most prominent of these towns is Arkham, Massachusetts, where a house isn't considered complete if it doesn't have five or six different dark secrets worked into its construction.
The Tcho-tcho people in T.E.D. Klein's "Black Man with a Horn". A missionary goes to investigate the people, who turn out to be very vile. However, the Missionary still doesn't know what the tribe is doing, and is sure they want it that way.
Ramsey Campbell sets his tales in the Severn Valley. Almost every town has some dark evil lurking somewhere, in various degrees. Some are hidden and the inhabitants ignorant, other evils are trapped, and then there's the whole towns in on the secret.
In Watership Down, the bucks arrive at a warren where everything seems abundant, though the residents act rather strange (for instance, there's a strong taboo against asking where anyone is). Later they discover that the warren is, in fact, a free-range rabbit farm, and it's common and widely accepted knowledge that rabbits are dying in snares. (The reason for this quiet acceptance is the tradeoff: complete immunity from all of Rabbitdom's non-human enemies, enforced at the end of a gun barrel.)
Graystone Bay in the anthology series edited by Charles L. Grant. A sinister foundation, and jam packed with weirdness, until it literally disappears in the fog.
Welcome to Dead House is about a teenage girl who discovers her new house is "The Dead House" to which a new victim is invited every year and devoured by the undead residents of the town.
In My Hairiest Adventure the town is run by a scientist, and all the kids there are actually dogs.
The town of Shadyside in R.L. Stine's Fear Street series. Teens dying horribly, being possessed by evil — and it's all going on for centuries.
Lesser Malling in the first book of The Power of Five series. The secret is that all the villagers are working to open a gate which will let the Old Ones, and the protagonist is one of the five tasked with making sure that such things don't happen.
There's also a village of cannibals in the last book.
The company town of Despair, CO. in Lee Child's Nothing To Lose. Its dark secret isn't (really) that the giant metal recycling plant is recycling munitions ("the government's dirty laundry"), bombed-out cars from Iraq, or even that they're helping deserting soldiers flee to Canada but its religious fanatic owner is stockpiling the salvaged uranium to set off a dirty bomb and jumpstart Armageddon by causing (even more) fighting in the Middle East. Their mistake is trying to run the Determinator protagonist out of town and leaving a deserter-turned-informer to die in the desert to be found by said protagonist.
Scrote in Terry Pratchett's Soul Music, probably. We never actually get it confirmed that there's anything sinister about their traditional barbeque near the rockery, because The Power of Rock protects our heroes.
In Brotherhood Of The Rose by David Morrell, the intelligence services of the world have set up several luxury "retirement" communities, each regarded as neutral ground where no-one is allowed to be harmed. Only the men running them know that the residents (ambitious men who've fallen from grace, cooped up in a gilded cage which eventually palls) are frequently Driven to Suicide.
The town of Omelas, from The Ones Who Walk Away from Omelas by Ursula K. Le Guin, must always keep a mentally handicapped child locked in a dark basement, given only the barest amount of food to survive, without any kindness or affection given to that child for any reason whatsoever, for the moment anyone gives that child any sort of comfort at all, their entire "Utopian" society will collapse in that instant. The story is unclear whether the child was born handicapped or has just broken from malnutrition, fear, and only a few moments of cruel human contact a day.
Silverdale, Colorado in John Saul's Creature is a quaint company town where the school has a high-tech sports clinic...which seems to be turning the kids in the town into 'roid raged monsters...
Dashiell Hammett's short story "Nightmare Town" (in a collection of the same name) seems like a weird town where people act strange, there seem to be more houses than people, and the guy running the town is openly threatened by his son. The secret is that it's run by, and for, murderers and thieves, and the protagonist happens to get there a few days before the place is burned down for the insurance money. It's one of the few examples where the secret isn't supernatural, and yet still manages to be just as much Nightmare Fuel. Only a handful of people don't know the secret.
Inverted in Good Omens. Lower Tadfield has a secret, but it's hardly dark. Superficially it's a quaint little Quirky Town complete with pristine cottages, white picket fences and apple trees, but it hasn't changed for ten years: Urban development bypasses it completely, the weather is always perfect, and the area is rich in ley lines. This is because it's the home of the ten-year-old Anti-Antichrist, who wants to keep it intact for his perfectly normal childhood amusement.
The Survivalist series by Jerry Ahern. In a post-World War III American the title character finds an apparently peaceful village where no-one even mentions the war. It turns out that everyone made an agreement to use up all available the resources to keep things going as before; when the supplies run out they plan to commit mass suicide by blowing up the town. Unfortunately by the time he finds out a woman whose husband has died has tied him up so they can die together.
Played with in W. D. Valgardson's short story Bloodflowers; what was originally a Quirky Town only became a TWADS after the narrator accidentally gives the superstitious townsfolk the idea to sacrifice him.
Peyton Place. Basically, the entire novel is author Grace Metalious's way of saying that every idyllic American small town has at least one dark secret hidden in its depths.
Jakub Wędrowycz stories feature a secluded village inhabited entirely by neanderthals whose progeny has somehow survived until modern times. To the outside world, they seem just to be a bunch of very ugly humans who hate strangers and don't pay much attention at the church (assuming that there is currently a priest there after the previous one has died in mysterious circumstances). In reality, they're half-animalistic, still worship their pagan deities and indulge into cannibalism, eating their dead.
Moonlight Cove, California in Dean Koontz's Midnight. It appears to be a quiet coastal village until you notice the ominously overprepared police force and hear about all the violent deaths in recent weeks. Turns out, Moonlight Cove is under the control of a megalomaniacal Mad Scientist trying to create a race of cold, efficient New People, and the remaining normal citizens are all scheduled for "conversion." Unfortunately, some of the New People have been . . . regressing.
Another Koontz example is Moonlight Bay in his Christopher Snow books, where the authorities are cooperating with the military to hide a massive, civilization-destroying secret.
Denke, Kansas, a town of cannibals in S.K. Epperson's Borderlands.
Haven: A Novel of Anxiety has the titular town in Idaho, which seems nice at first, but is full of racists who massacred Chinese miners in its early days and harbored Nazis after WWII.
In Norman Partridge's Dark Harvest, all the teenage boys of a small Midwestern town are entered into a Deadly Game with a murderous pumpkinheaded scarecrow named the October Boy. But wait, that's not the secret.
The real secret is that every winner of the game is actually set to be killed by their father in order to become the new October Boy, and the father is then expected to help put the boy together when the next game begins. The protagonist ends up helping the latest October Boy when he learns the truth.
In The Halfblood Chronicles, the treatment of humans by the elves that run things generally ranges from chattel to cattle. The third book, Elvenborn, introduces the estates of House Prastaran... which handles things in a manner far closer to unusually egalitarian/idealized English squiresnote (most human slaves capable of contemplating running away have to defeat enspelled collars and flee into the wilds; here they need merely give notice and their lordships will smuggle them out) and have to put considerable effort into stage-managing the visits of outsiders.
This also occurs in Mitchell Scanlon's Horus Heresy novel Descent of Angels. A planet has been delaying their full compliance with the Imperium for years now, all the while hiding the presence of their xenos overlords. Ultimately, they've been buying time to summon an Eldritch Abomination to defeat the Imperial forces.
In the Wheel of Time, Mat and the Band run across the town Hinderstap, where the people are zombies who go apeshit every night and kill each other, but wake up in their beds the next morning regardless.
The town of Wind Gap in Gillian Flynn's "Sharp Objects."
The town of Golgotha, from Six Gun Tarot has many, many dark secrets, from the vampire in the unmarked grave to the head in a jar upstairs of the general store. And that's leaving aside the Cosmic Horror from beyond time and space buried in the old silver mine.
In The Altruistic Personality by Samuel P Olinger, the author says that there were a few small hamlets during World War II where rescuing hapless fugitives was almost the town's chief industry.
Live Action TV
Smallville. The charming little town is plagued by a million and one various threats, but the wave of psychotic meteor freaks brought about by the first meteor shower is closest to this trope. Most people know that there is something wrong with the meteor rocks and many witnessed its effects on people, but a lot of them seem to live in denial or blame it on the LuthorCorp experiments.
Haven, Maine - A small town that hosts various cursed individuals. The mysterious 'Troubles' have recently returned, causing the deadly powers of some citizens to reactivate with horrible consequences. Loosely based on (well, uses some names from) a novella by Stephen King.
The made-for-TV-movie The Disappearances has, among other things, a ghost-town with a secret. The sheer volume of red herrings presented eliminates the ability to accurately figure out what that secret is, mind you, but it's most assuredly there.
This is the essential plot of Eureka, where the eponymous town is the site of a top-secret government research facility. The tagline for the first season was "Small town. Big Secrets." (Though it's portrayed as more of a Quirky Town despite the Death Ray, runaway Nanomachines and other Phlebotinum Overload that happens on a regular basis.)
In Stargate SG-1 episode "Nightwalkers", the team arrives in a mysterious town to investigate the disappearance of a scientist. The townspeople are alternatively friendly and hostile towards the protagonists and it is revealed that the whole town was taken as a host by Goa'uld symbiotes, including the scientist who had originally given the alarm. However, the townspeople themselves were not aware of this as the symbiotes take control only at night.
Jon Stewart on The Daily Show mocked the "this town holds a Dark Secret" advertising for Wolf Lake by saying "Let's ask the werewolves! Maybe they know what the Dark Secret is."
Subversion: American Gothic has Trinity, SC, a town whose dark secret is that its sheriff is the Devil Incarnate. But no one knows this fact at all (except Merlyn, it seems), while only the few who run afoul of Buck's wrath, dare to cross him, or refuse to obey him ever even discover what a Magnificent Bastard he truly is. On the other hand, there are quite a lot of people in town keeping their own secrets: Dr. Crower, Gail, the coroner, the priest, Ben, Selena...
Subverted in the case of Sunnydale. It's a sizable city instead of a small town. Instead of everyone being in on the dark secrets (the portal to Hell, the various demons and vampires that treat the place like a buffet and the buried [sometimes magical] treasures hidden in the right mausoleum), most of Sunnydale's citizens are hilariously oblivious/in denial about the many, many mysterious deaths that occur there. The only humans in on it are various characters who tap into the dark powers of the place for their own ends, such as the Big Bad of Season Three. The secret government lab under the college is the least exciting secret there was.
Pretty much every small town the Winchesters visit in Supernatural. For some reason, it seems that you can't become a person of respect in your town without having committed some horrific act in the past.
The village in the Brecon Beacons in the Torchwood episode "Countrycide".
In the Roswell episode "Harvest" (2nd season) the main characters travel to the suspicious town of Copper Summit, Arizona — which turns out to be filled with their alien enemies.
The suburbs in Chuck vs. the Suburbs. It turns out that everyone in their cul-de-sac is an agent of Fulcrum, a criminal organization.
In "Murdersville", an episode of The Avengers, an entire town conspires to offer outsiders the opportunity to stage a murder. The townsfolk will serve as alibis and help dispose of the remains afterwards, in return for a sizable sum of money. (The villagers who refuse to participate are kept locked up in ancient torture devices in the town museum.)
Played for Laughs in the Ripping Yarns episode "Whinfrey's Last Case". It turns out that all the inhabitants of the Cornish fishing village where agent Whinfrey takes his holiday in 1913 are in fact German spies. What's more, this turns out to be part of a conspiracy between the British and German Governments.
Happy Town tried very hard to be this to the point that they ended up making it fit the title while advertising heavily to be certain absolutely everyone knew it was a Sarcastic Title.
Morton Harwood in the Doctor Who spin-off K-9 and Company. Well, if cheerfully explaining to visiting reporters "They're a bit sensitive about that [devil-worship] around here. It's traditional, you see." counts as a secret...
One episode of The Rockford Files features the town of Pastoria, which traps wealthy travelers in the town, frames them for an absurd number of crimes, then convinces them to plea bargain and pay a large fine to the city instead of going to jail.
The sleepy English village of Little Stempington from Suburban Shootout seems unbelievably clean, genteel and old-fashioned- until you find out that it stays that way because of gun-toting housewives threatening anyone who affronts their middle class values.
The X-Files episode "Our Town". The Arkansas town of Dudley is entirely made up of cannibals who kidnap, kill and eat human beings in order to maintain their youth. They accidentally eat a victim who has Creutzfeldt-Jakob disease and become infected with that syndrome.
Storybrooke in Once Upon a Time, in which nearly everyone is a Fairy Tale character brought into our world through a magic curse, though none of them remember. Though most of the inhabitants are decent people, the mayor is the Evil Queen from "Snow White" who frequently abuses her power through both mundane and magical means. Even after the curse is lifted, everyone gets their memories back, and the Queen is deposed, Storybrooke still fits the trope as the citizens work together to keep outsiders from finding out who they are.
In case you were wondering about LazyTown, it has a dark secret of it's own. In the old days before the active warriors came, LazyTown was lazy. No fitness, no healthy things, NO NOTHING. Every mayor until the active warriors came were part of the family of the "evil dude"(who was the last of his family to be mayor of LazyTown before the warriors put him in a prison & buried him deep underground.
The town of Maiden Creek in the Miss Fisher's Murder Mysteries episode "Death on the Vine" has a secret regarding the death of a German farmer at the end of World War I. Phyrne Fisher steps into the middle of the secret when the farmer's son calls her in to investigate, only for her to find that he has been murdered by the time she arrives.
The lovely Virginian town of Mystic Falls is a wonderful place to live, with frequent town festivals and friendly locals. The only danger is the frequent "animal attacks", which certainly aren't excuses contrived by its Council and the town's founding families to conceal its recurring vampire problem.
Warhammer 40,000 favors the Planet With A Dark Secret approach instead, with roughly even odds of Chaos, Eldar, Genestealers, and/or Necrons being said secret. Since we're talking about planets here, there's plenty of room for multiple dark secrets to be hiding out, all of them unaware of one another.
The core rulebook features a story about a town where every year, several people die without any explanation, and they encourage the new-in-town priest to quietly accept it. He doesn't get the hint until Death himself shows up to tell him to shut up and sit down. However, for those who are Genre Savvy, it is implied that it's actually a vampire using Dominate. The way he looks and how he manages to "freeze" the poor priest in place does look like something a vampire could do...
The quevari appear as normal, pacifistic human beings most of the time, seemingly untouched by the evil that surrounds them. Until the three nights of the full moon that is, when every man, woman and child turns into a bloodthirsty killer. They've learned to block out what they do when they change, and never speak of it (even to travelers).
Considering its Gothic horror theme, it'd be hard to find a town in Ravenloft that doesn't have a dark secret.
In Dogs In The Vineyard, the PCs are sent by an Expy of the 19th-century Mormon church to visit a series of towns. They have some simple duties, like healing people and delivering the mail, but the interesting ones (i.e. the ones you actually have game sessions for) are either headed for this trope or already there, and the PCs have to fix it by any means necessary before it falls into full-blown demon-fueled Hate and Murder.
Call of Cthulhu supplement Dreamlands, adventure "To Sleep, Perchance to Dream". Everyone in the small Vermont town of Bensamin is a Cthulhu Mythos cultist. After the PC Investigators are lured there, they're captured by the townsfolk and kept as future Human Sacrifices.
The musical Brigadoon (first produced in 1947). Although Brigadoon is more of a Lotus-Eater Machine that happens to be real, depending on how one looks at it.
Ironically, Silent Hill in the film adaptation is inspired by the Real Life small town of Centralia, Pennsylvania, whose citizens accidentally set a coal seam on fire by burning trash and never bothered to tell anyone about it until a child nearly fell through the ground and into the fires below. It's nothing more than a smoldering Ghost Town now.
The village on the island with Balduran's ship in Baldur's Gate. Which is not so secret anymore, since anyone simply refers to it as The Werewolf Village.
Zevran:"Just once I'd like to walk into one of these places and discover a lively dance, or a drinking festival. Or an orgy. But alas, no."
Final Fantasy VII's Nibelheim. After the town burned to the ground as a result of the Super Soldier Sephiroth going off the deep end, Shinra, Inc. had the whole place rebuilt and populated by hired actors in an effort to hide the fact that the entire incident ever happened.
In The Secret World there is an entire three-part zone that is basically a huge Lovecraft Shout-Out (complete with the Ur-Draug, a Cthulhu Ersatz as a dungeon boss). One of the zone parts is Kingsmouth - a small, cozy town that's currently under a zombie and draug attack. There are lots of quests that let you dive into the town's history - and while there is apparently not one, huge secret, there has been a LOT of creepy things going on through the years. This is also lampshaded by several NPCs.
In The Elder Scrolls IV: Oblivion, there's a minor town you have to visit after a merchant's daughter disappears there. The Church has a book dedicated to "the Deep Ones", and people say things like "the Brethren don't take kindly to strangers. I'd leave before they find out you're here." If you spend the night in the inn after asking questions, you wake up in the middle of the night to find yourself under attack by some cultist, then can find your way into the underground to discover that the shopkeepers daughter is about to be sacrificed for an unknown reason. A demonic summoning, perhaps?.
The first town you come to is mostly abandoned except for demons and tormented souls. The town fits this trope all the better considering that they, you know, are the bitter souls of abused domestic animals who want to eat you. That certainly puts a damper on things. Funny thing: Yuri knows this going in, but he doesn't care, because he knows he can deal with it.
Bistritz is another one — but the secret isn't the vampire up in the castle (he's a Friendly Neighborhood Vampire), it's the experiments being conducted by the mayor, which are waking up monsters.
The eponymous village has a secret, though it isn't dark - nearly all the inhabitants are robots, and the village itself is designed to keep Baron Reinhold's daughter Flora safe until a suitable caretaker appears for her.
The second game had a town with a secret too: the village of Folsense (and maybe the townspeople) is one giant hallucination.
The trend continues into the third game: Future London isn't London from the future at all, it's a city in the present located underground the actual London.
The town of Doolin in Folklore is known as a place "where the living can meet the dead." This is only kind of true, but in the course of trying to get to the bottom of what really does go on in Doolin, protagonists Ellen and Keats uncover a few other nasty secrets revolving around a series of deaths and disappearances which took place seventeen years previously on the night of Samhain.
The town of Pyrewood is home to Alliance-friendly NPCs during the day, who turn into bloodthirsty Worgen that attack anyone on sight at night.
Silverbrook in Northrend: The town inhabitants are actually Worgen who act friendly towards you, in hopes of turning you into one too, but you get better, and they get hostile. After this every trapper settlement is hostile to player.
Fallout 3's Andale. Best town in the (destroyed) US, fresh baked pie every morning, and cannibalism. And a long tradition of incest among the TWO families in the town.
It looks like Charwood is one of these in Neverwinter Nights. It's actually only the noblemen who have the secret, and the townspeople have just been screwed over by it. And then you find out that the nobles themselves were screwed over by Belial.
In Darklands, the events take place in medieval Germany. The protagonists begin the main quest by finding out, which of the many villages has a Dark Secret of being populated by devil worshippers. Attending the mass there is particularly creepy...
That and as has been pointed out in reviews. Just when you think you can recuperate from your injuries in a small village you might well wake up in the middle of the night to find them trying to sacrifice you to demons.
Early in Final Fantasy IX, the characters enter the town of Dali, where they're secretly making Black Mage constructs for Queen Brahne that bear a strong resemblance to one of your characters.
Around the start of Chapter 3 in Terranigma, you go to Louran, a nice little desert town with nice people and a lot of ambitions. Until you find out that Louran's been destroyed for quite a few years now and all its inhabitants are actually zombies. The nice town you saw was an illusion by a girl who used to live there.
All of the zombies themselves are also illusions by the girl (who can somehow hurt and even kill you) that disappear forever once you find her, and nobody actually lives there at all.
There's also Crysta, which is a copy of Storkholm in the Light World complete with copies of its original inhabitants. Near the end of the game, the villagers and chickens turn into spirits and attack you if you talk to them (doing no damage). You can kill them by throwing things at them, but they regenerate. They also drop massive amounts of gold which is completely useless by this point of the game, as there's nobody to buy anything from (Crysta's shopkeepers aren't exactly eager to help).
The First Town of The Witcher, the outskirts village of Vizima, apparently plagued by beastlike ghosts possessing dogs. Though they blame the local witch, she simply sold them the implements the corrupt people demanded to curse themselves with. The town elders are collaborating with and selling their children to a vicious mob who casually murder the citizens. There are definitely ghost-dogs and the like, but the dark secret is WHY they are there.
Mass Effect series:
Zhu's Hope in Mass Effect 1. The colonists are all mind-controlled by the ancient plant creature that lives beneath the city.
In Mass Effect 2 Samara mentions another example of this trope in her backstory: a small asari colony that had been seduced by an Ardat-Yakshi, an asari with a rare genetic mutation that causes her kill anybody she has sex with, who feature prominently in their mythology as evil gods and anti-heroes. She had convinced the entire colony to worship her as goddess, and sacrifice their young Maidens to her, and when Samara came the entire colony save for the youngest children threw themselves at her to give the Ardat-Yakshi a chance to escape.
Mass Effect 3 has Sanctuary. Supposedly, it's one of the last safe places in the galaxy in the face of the Reaper invasion. In reality, it's a Cerberus facility, run by Miranda Lawson's evil psychotic dad. All the hapless refugees are getting experimented on. And then the Reapers show up...
Fatal Frame. Some of the things that happened to outsiders were unpleasant, before and after the communities' imminent demises.
Dragon Quest VII has present-day Labres: the town features a monument boasting about the heroic villagers protecting one of their own from some terrible travelers who tried to slay the transformed man. But this version of events is a complete lie — the truth is that they lynched the poor man, and threw a child and the travelers who tried to stop them to the real monsters. The monument was originally meant to remind them of their greatest failure, but corrupted and turned into a feel-good lie to drum up tourism. Ultimately, you discover the real monument, only for the mayor to destroy it — but not before their children all get a chance to read the true version of events and swear to spread that version instead, even against their parents' wishes.
Kakariko Village in The Legend of Zelda: Ocarina of Time. The place is home to not one, not two, but THREE of the creepiest places in Hyrule, the Bottom of the Well, the Shadow Temple, and the House of Skulltulla. Unlike most examples, the town's inhabitants seem blissfully unaware of all the strangeness going on underneath them, but otherwise it fits the trope perfectly.
Harvester: The town of Harvest. It is clear from the get-go that Harvest is not a nice place to live, and nobody even tries to hide that. Despite this, it does contain a Dark Secret like you would not believe. The town of Harvest does not exist. It is just a virtual reality program that Steve and Stephanie were hooked up to. The entire program is a murder simulator and it is supposed to slowly and surely turn Steve into a Serial Killer. He can get out of the program... if he murders Stephanie and makes her Killed Off for Real.
The Elder Scrolls V: Skyrim has the hold of Markarth, which has not one, but TWO dark secrets: A good number of people in town are Forsworn infiltrators and most of the rest are cannibals who worship the Daedric Prince Namira.
Not to mention the haunted house with a shrine to Molag Bal in the basement.
Vale, the heroes' hometown, seems to be one of these to outsiders in the first game due to The Masquerade about Psynergy. This apparently gets dropped between The Lost Age and Dark Dawn, when Vale's destruction causes its people to move to Kalay and word gets out about Psynergy.
The Secret of Monkey Island. The island seems pretty peaceful (even the cannibals eventually bargain with you). That is, until you discover The hellish labyrinth beneath the giant monkey head.
Story Of The Blanks starts out as a seemingly bright and cheerful My Little Pony: Friendship Is Magic flash game where Applebloom encounters a nice place called Sunnytown and talks to the inhabitants. Then it hurls the player on a bus straight to Creepy Town and ends with poor Applebloom fleeing a cursed village while its undead inhabitants chase her down.
Deadly Premonition takes place in the town of Greenvale, the site of a murder that brings in FBI agent Francis York Morgan. Morgan eventually discovers two important things about Greenvale: several decades ago Greenvale was used in a government experiment involving a drug that made people insane, and the current sheriff runs a tiny S&M cult and forced several of the women in the town to be his sex slaves.
Shadowgirls: The original Innsmouth, an early example of this trope, was a decaying hovel of mutants and secret cults. In Shadowgirls, however, its modern-day incarnation appears to be a perfectly ordinary coastal town. But don't let appearances fool you: the Esoteric Order of Dagon still controls most of the government and Deep Ones lurk off the coast.
Sturmhalten. Everyone may not be in on it, but except for the ruling family, and apparently a few nobles, the town's entire population is made up of revenants. And the Prince is trying to resurrect the Big Bad. By abducting every female Spark he can get his hands on to try to give her a new body. Including his own daughter. Who has her own plans to wrest control of said revenants and the Big Bad's other minions. It may be easier to just list the things that weren't Dark and Secret about the place.
Mechanicsburg; Not only is it populated entirely by minions waiting for their masters to return, but it's a Genius Loci built on top of a holy spring known for causing insanity and death.
Podunkton from the Sluggy Freelance arc "Phoenix Rising" is secretive to the point of parody about its past as a mafia controlled town, or the current state of its vigilante based peacekeeping.
The citizen's of Richard's village in Looking for Group are all ravenous undead capable of slaughtering common mortals with ease. Even the little girls can rip out a man's heart.
"We call it Pretty Pretty Unicorn. It's a work in progress."
Kit N Kay Boodle's Yiffburg is one, though their method of "secrecy" is simply being too ridiculous for anyone to take seriously as a threat. The comic is drawn in a cutesy, cuddly, cartoony art style, but when the candy coating is washed off, the end result is that the main protagonists are very dedicatedly out to conquer the world and convert it to mindless sexual hedonism in the name of their gods- however, they don't tell that to anyone outside their Sugar Bowl town, because the rest of the world won't openly oppose them as long as they're only complaining about what lazy perverts they are instead of actively trying to stop the spread of their cult.
In Lovecraft Is Missing, Tough Luck, Oklahoma is revealed to have its own Cthulhu cult that meets secretly in an old barn.
In No Rest for the Wicked, the protagonists come upon an unnamed village where the villagers believe that there is a witch in the forest who has abducted and murdered huge numbers of their children. They're right, but the thing is that the children weren't entranced into the forest by the witch's magic, the villagers have been abandoning their children in the forest to die (in some cases) or they've intentionally not done anything to prevent their children going in of their own volition. Once November, Perrault and Red kill the witch and bring the only living children back, they leave the villagers with their guilt.
In the Whateley Universe, Whateley Academy is literally in Lovecraft Country, since the closest town is the Dunwich. Only maybe half of Dunwich is in on the dark secrets, since the town has been gentrified.
In The Terrible Secret Of Animal Crossing, the protagonist finds himself on a bus to a camp under strange circumstances, and bit by bit, the secrets of the camp's much-too-happy exterior finally come to light. Even the final chapter is aptly named, "All's Well That Ends."
SCP-599 ("Uncharted City"). Exactly what the Dark Secret is is never directly stated, but it's implied that the town is a malevolent Genius Loci that lures people in, then kills them and integrates them into itself as citizens.
SCP-1948 ("Weather Bird"). SCP-1948 is a bird that creates nice weather to keep itself comfortable. The town sacrificed people to it whenever the weather got worse, not realizing that it was responding to El Ni˝o and would return to normal once the system had passed.
Night Vale is an Eldritch Location where time doesn't work properly and members of a shadowy, all-powerful government routinely practice their public speaking skills by denying the existence of things like cars and eggs, so as to more easily deny the existence of things like three-headed graffitist dog packs, the illegal use of public funds to raise the ghost of Syd Barrett for a private Pink Floyd concert, and angels. However, every citizen seems to be cheerily aware of these facts, so maybe it's not so secret after all. This trope may apply more to the neighboring town of Desert Bluffs, which is even more horrific than Night Vale, but the radio host there speaks so cheerily that we'd never know about the pulsing meat walls, smears of blood and handfuls of teeth that decorate his studio.
Both Towns seem to have Dark Open Secrets. Everything is expected to work like usual, except stated otherwise, by the audience, but... is it their usual our our usual?
Scarfolk Council Scarfolk is a town in North West England that did not progress beyond 1979. Instead, the entire decade of the 1970s loops ad infinitum. Here in Scarfolk, pagan rituals blend seamlessly with science; hauntology is a compulsory subject at school, and everyone must be in bed by 8pm because they are perpetually running a slight fever. "Visit Scarfolk today. Our number one priority is keeping rabies at bay." For more information please reread.One of "The 100 Funniest Things in the History of the Internet"- GQ Magazine http://www.scarfolk.blogspot.com
"There is no war in Ba Sing Se." If the Earth Kingdom is the Fantasy Counterpart Culture of China, then Ba Sing Se, the capital, is more like the modern PROC or North Korea. It's a perfectly safe city, full of culture, divided into separate districts, where the guides smile all the time. Oh, and the poor and undesirable are walled in, people are forced to deny there's a one-hundred-year old war going on, and anyone who starts asking too many sensitive questions gets disappeared and brainwashed.
Jet's treetop village. "Oh, cool, a settlement of teenage rebels! Maybe they can help us fight the Fire Nation!" Only problem is, these Well Intentioned Extremists often take their rebellions a little too far...like, oh, I don't know, when they beat and robbed a harmless Fire Nation civilian, or when they destroyed an entire Earth Kingdom town just because it was occupied by the Fire Nation army.
Justice League has Seaboard City, a town in an Alternate Universe that serves as an Affectionate Parody of the Golden Age Of Comic Books. It's later revealed that the whole thing is secretly under the control of a tyrannical, reality-warping child named Ray Thompson. After a nuclear war devastated their planet, Ray went mad and used his powers to recreate Seaboard City as he remembered it, forcing the remaining survivors to play along with the illusion or be killed.
The first episode of The 13 Ghosts of Scooby-Doo has the gang enter a town where everyone turns into a werewolf at night as a result of a curse put on them by the demons of the chest. They try to get the gang to leave to keep them from finding out about it, then try to keep them from leaving once they find out. Luckily, Flim-Flam manages to cure everyone.
Crystal Cove in Scooby-Doo! Mystery Incorporated, the town hides a dark secret to which is connected to the Planespheric Disks. To which the old Mystery Inc would kill over for.
The town of Gravity Falls, Oregon is home to everything from magical creatures to government conspiracies, which are slowly uncovered with the help of a journal the main characters founnd in the woods.
In one episode of The Real Ghostbusters, the heroes were unlucky enough to encounter a town called Lupisberg, which had three dark secrets. The first one was, the inhabitants were vampires. The second one was, the vampires inhabiting the town were feuding with another clan of vampires (not that the other clan was any better, mind you). The third secret was, both clans of vampires had taken over the town from the original residents, who were werewolves, and imprisoned them under the town. After the heroes released the werewolves who were dead set on taking their town back, the heroes were smart enough to high-tail it out of there.
Taiji, a town located in Higashimuro District, Wakayama, Japan, conducts an ongoing dolphin hunt off its coast (as made well-known in the 2009 documentary film, The Cove). Mercury levels among its citizens are much higher than average as a result of the sale and consumption of dolphin meat in Taiji. The film depicts a cover-up orchestrated at all levels, from the fishermen themselves up to the town's mayor, revealing a town striving to hide its dark secret from the rest of the world.
Colorado City and the other compounds of the Fundamentalist Church of Jesus Christ of Latter-Day Saints (FLDS, not to be confused with the LDS church, aka Mormons), at least until their polygamy, child weddings, and abandonment of teenage boys became public knowledge through several high-profile raids in 2009. Still, they tend to be very hostile to visitors, with news reports showing residents running from cameras and police officers attempting to arrest the reporters.