If all you know about Higurashi is the cover, you will be very surprised by the beginning of the first episode, and troubled by the vaguely sinister opening credits, but the bulk of the episode will seem like a typical Slice of Life comedy featuring a boy who has recently moved to a cheerful small town and befriended four female classmates... but before the first episode is over, the boy has realized he's living in a Town with a Dark Secret, and everything starts spinning out of control, and by the end of the fourth episode, half of the main characters have died gruesomely, including the Decoy Protagonist, and you realize the beginning of the first episode showed you that this was going to happen. And then the fifth episode begins with one of the younger main characters stabbing herself to death with a huge knife for no apparent reason, and after the opening credits, it's back to light-hearted comedy.
Tenshi Ni Narumon: Painfully sweet, cutesy, silly and looks like it was made for some toy store line. By the end of the series, the darkness, creepiness and mindfuckiness will make many cringe. And there's a pretty explicit yaoi innuendo going on there too.
Dai Mahou Touge (or Magical Witch Puni-chan) features a magical princess sent to a high school in the human world as part of her princess training. She has a cute talking animal side-kick, a magic wand, and the ability to animate vegetables into evil minions (or to jump into whatever she's cooking). This adorable little girl wrestles opponents with the intention of breaking bones, says "submission is a princess's way!", and her animal sidekick, who was forced to be her pet after she kicked the tar out of him, constantly wants to kill her. Within the magical kingdom not everything is so magical; for instance, an army of slaves is used to move trains. None of this is ever shocking to Puni, but her normal human companions are often either stunned or frightened.
School Days starts out as a cute teenage love story about a guy trying to get a girl with help from his female friend. When he does finally get her, he does a bad thing, and things spiral out of control as the series gets much darker and depressing and loses all traces of its cheerfulness. This all culminates in the final episode with his girlfriend, having just murdered his female friend, snuggling his disembodied head.
Momotaro's Divine Sea Warriors starts out as a cutesy film with adorable animals, but once the title character shows up it turns into disturbing war propaganda.
The first Unico movie starts off with a bunch of cute baby unicorns, but ends with Unico impaling a demon and sending him straight to Hell.
Paperinik New Adventures: Hey look, a comic with Donald Duck as a superhero. Man, this is gonna be so funny... Wait, did those alien vampires just conquer an alien world and transform everybody into zombies? And now they are heading toward Earth?
The My Little Pony: Friendship Is Magic fangame Story Of The Blanks starts out as a nice, interesting little game starring cute little Apple Bloom finding a town full of blank flank ponies in the Everfree Forest. Then you find a skeleton in the fire place. And that's just how the scary part STARTS.
Super Filly Adventure is a fun little My Little Pony: Friendship Is Magic fangame that has you attend one of Pinkie Pie's parties and save Ponyville with your flank-kicking combat abilities. Even the "bad" ending where you become so obsessed with baking muffins that Ponyville burns down is far more silly than disturbing. Then you discover the secret "Blank Flank" ending, which is accessible only if you play the game at a very late hour...
The Pony POV Series chapter "Playtime" is mostly lighthearted, focusing on the Mane Cast talking with Princess Gaia as if she were simply Fluttershy and the foals that Ponyville has been turned into just playing around. Then Princess Gaia's facade shatters, revealing her true form, NightmareWhisper.
Marie D Suesse And The Mystery New Pirate Age starts off like a "Girl falls intoOne Piece" adventure, until the main character finds themselves alone on the Thousand Sunny with the crew mysteriously gone missing. Then weird things start happening, a disembodied voice starts singing, and the hostile Klabauterman shows up... Things only get darker and creepier from that point on. It's all the more unexpected because based on the first chapter and summary you would have thought the story was just a Mary Sue parody.
Moonstuck, aside from the occasional appearance of Dark Woona, is a silly and fun romp across the moon with Woona making lots of friends and things that don't make sense. The final boss fight, and the lead up to it, is shockingly dark and depressing even without comparing it to the rest of the story, with one of the most terrifying portrayals of Discord that the fandom has ever produced.
The film version of Watership Down starts out with a fun and interesting myth about the creation of the world by Frith and how the rabbits and other animals came to be. Then we flash to the main plot and get a group of animated rabbits, and it all looks like an enjoyable kid's movie about cute little bunnies until suddenly Fiver mentions something about the field being covered with blood. It quickly goesdownhillfromthere.
Meet the Robinsons. The first 3/4s of the movie are full of colors, gleeful wackiness and literal bubbles. Then, just after what appears to be a daring rescue, the robot friend gets speared through the chest and dies, the main character's best friend/future son disintegrates into nothingness, the world is plummeted into despotic despair and slavery, and the main character's family, being controlled via electronic hats that cover their faces, starts trying to kill him by beating him off a very high fall. All in the space of about two minutes.
Pinocchio is the story of a cute little puppet boy and his journey to become human... which leads to the Pleasure Island subplot, which involves other boys getting lured into a seeming happy-looking place where they can misbehave and do what they want, but then get turned into donkeys and shipped off to work themselves to death. We see a nightmare-inducing sequence where one boy screams and begs for help as he slowly and painfully transforms.
The same goes for Matilda, with its freaky wide-angle closeups and uncannily cartoonish torture/violence.
ParaNorman is mostly a Fantastic Comedy about hilariously ineffectual zombies and living characters who aren't any more competent, though the very realistic bullying Norman suffers stops it from being fully a comedy. Then the true nature of the "witch" is revealed, and suddenly everything in the film becomes a lot more horrifying.
The dead from Corpse Bride are anything but scary or even creepy. They're lively, upbeat, and a hell of a lot more fun to be around than the so called living. Then they find out it was Lord Barkus who murdered Emily and suddenly careen rapidly into horror town, ending with Miss Plumm ominously saying "new arrival" as they literally drag him to hell.
The fantasy novel series Fablehaven. Despite its bright and cheerful kid-aimed covers, it gets smacked upside the head by our friend Cerebus remarkably quickly. Each book is darker than the last, but the covers remain cute and inviting.
The Candy Shop War by the same author has an arguably more kid-friendly cover, but is just as dark.
Olivia Kidney has a title protagonist who appears on the cover as an adorable, cartoony little girl. She talks to ghosts all the time, including her beloved dead brother. There's the ever-present implication that everything that's happening might just be a product of an extremely overactive imagination. Or maybe it's all real. They never really let you know for sure, and it's not clear which would actually be worse.
Redwall starts out seeming like a sweet little Low Fantasy series about cute fuzzy animals in a pretty woodland setting. Then some pretty damn horrifying things happen to them. It says quite a bit about this children's series that it was the first work of literature to get its own Complete Monster page.
When unhappy or unpleasant truths intrude on the relatively peaceful lives of characters in the Aunt Dimity cozy mystery series, they often do so in this way. Open a box expecting to see maybe an heirloom—find fully dressed human remains. Heave a sigh a relief that the "murder" turns out to have been an accident—well, that's jolly nice, but your hero has just had a flashback on a real murder he witnessed and is near catatonic. Similar mood dynamics occur when solutions are given and the culprit turns out to be obsessed and/or insane.
Harry Potter starts off as a whimsical children's series, then takes a very dark turn in book 4. The author even noted this idea by pointing out the book started with a double murder but is still called a children's story.
Dr. Seuss wrote Thidwick the Big-Hearted Moose, which ends in Thidwick's unwanted guests being killed and taxidermized.
Nintendo and their development teams may well be the reigning champions of this trope. They have a family-friendly, even kiddy image, but quite a few of their games are clearly intended for brave kids.
The Legend of Zelda - Primarily E-rated games. E-rated games that include, among other things, a temple dedicated to death, zombies that are either trying to eat or rape the protagonist, and the apocalypse. Probably the two most blatant examples are Ocarina of Time and Majora's Mask. The ESRB seems to have caught on by the time of Twilight Princess, but even so its T rating was probably just because of the darker graphical style, since Skyward Sword has an E10+ rating despite not being too much more lighthearted.
Just when we thought Nintendo made The Legend of Zelda: The Wind Waker specifically to be absolutely and completely harmless, along comes Link stabbing Ganondorf in the brain. And when you consider how incredibly dark the backstory of this game is, it suddenly seems like the game's happy atmosphere was taunting the past and the people of ancient Hyrule, much like how the happy music in Clock Town seemed to taunt the people who stayed oblivious to their impending doom, only more subtle.
Skyward Sword has its moments too, most notably in the Ancient Cistern. At first it seems a bright and pleasant place with lots of clear water and green and gold scenery. And then you descend into the lower parts... Which culminates in Link climbing a rope to escape only to find that a horde of zombies is also climbing that same rope... and then you learn that to continue, you have to go back down that same rope.
Pikmin - More E-rated goodness that involves sending adorable little carrot-creatures to near-certain doom against beasts many times their size. In the first game Olimar does this to survive. In the second, it's all about getting treasure. Some of the more bizarre enemies in the game include a frog-shaped embodiment of poison and the moaning intangible Eldritch Abomination known as the Waterwraith. Olimar actually does wonder:
Would this have been a peaceful planet had I never come? No... Surely the Pikmin lived like this before my arrival. They MUST have.
Pokémon Mystery Dungeon: Explorers of Time/Darkness/Sky - A game which starts out with cute little monsters, in particular the nervous partner character, learning how to be good explorers. Starts getting a little uncomfortable when a child is abducted by a criminal, gets out and out distressing when you get dragged into the future, and the game really doesn't let up on the creepy for the rest of the story. You and your partner are encouraged to commit suicide at one point! Yep, E-rated.
The first Mystery Dungeon were already pretty creepy, like when all your friends suddenly turn on you and chase you for what seems to be days, clearly intent on killing you. And then there's the tale of Gardevoir's past...
The mainline Pokémon games themselves have started to get in on the fun, especially with the creepier Pokedex entries - see entries like Yamask and Shedinja's just for starters. Then there's Pokémon Black and White... would you like a nice cup of horrific psychological abuse of a child with your cute monster battling?
Pokemon Diamond, Pearl, and Platinum has pretty creepy moments as well. In all three games there are fun adventures, cute friendly monsters, and an evil cult that wants to destroy all of existence so their leader can reshape the world in his image and become God. Oh, and did we mention that Platinum contains an extra segment in the main storyline where you end up in a parallel universe and face off against a massive Eldritch Abomination of a dragon?
Pokémon Red and Blue's Lavender Town. Between the background music being more unnerving than it should be possible for any 8-bit song to be and the sudden revelation that Pokemon can actually die, there's the entire origin story of Cubone/Marowak and its/their skull-helmet thing. Not to mention the Cinnabar lab and the vague bits of Mewtwo's backstory we learn there.
Pokémon X and Y brings us to the Kalos region, a lovely region where great emphasis is placed on beauty and harmony. Then we find out about the various wars that took place there. Oh, and the evil team wants to use an ancient superweapon to effectively nuke the entire country.
EarthBound. 99% Cartoon-y goofiness, 1% incomprehensible cosmic horror. And it's the last 1%, too, especially because of the final boss...
Mario gives Link a run for his money throughout the Paper Mario games, which end up a lot like Earthbound with the subject of murder (though he was actually just unconscious) dealt with in the first game; an Eldritch Abomination appearing as the final boss of the second; and the third's plot being explicitly that reality itself was being destroyed, later revealed that this includes The Afterlife. Also notable is Super Mario Galaxy which is hours of compressed sheer joy — and then the universe is annihilated in a supermassive black hole.
The Kirby games feature a very cute eponymous protagonist, colorful and fanciful levels, and lots of frightening bosses. One of them is actually named Nightmare, and he's not even the scariest by the long shot! Perhaps most infamous among them are Marx Soul, especially his death sequence, and Zero, mostly for his Clipped Wing Angel transformation. Kirby 64 continues the tradition; while Dark Matter and especially the possession scenes are at least unsettling, they still don't provide any good warning for the jarring final boss. It took Kirbys Return To Dreamland to finally jack up the age rating to E10+, and the games mentioned earlier only got an E10+ rating when the Kirby Dream Collection was announced. For reference, that's over a decade since their original releases.
Magical Starsign. The game is saccharine and kid-friendly through-and-through until Semolina commits suicide through a carnivorous flower before you get a chance to protest, and becomes one of your Cosmic Keystones. Later, you get to learn the fate of Applepie, and/or every human in the universe once the robots start to run out of fuel: robots turn humans into "gummies", their battery cores. And that's ignoring the star-devouring abomination that is the Final Boss...
The Wii U-exclusive Game And Wario is a collection of fun, lighthearted minigames based around characters from the WarioWare series. One of the minigames, "Gamer", involves 9-Volt secretly playing WarioWare microgames whilst in bed. 9-Volt's mother 5-Volt occasionally checks in on him, and he must hide from the mother while simultaneously playing the game. At first glance, the game is not all that creepy, especially during the tutorial, and the mom is kinda cute looking◊. But the actual game has the mother check in on 9-Volt in several very creepy ways, including popping out of the television (with ominous static immediately beforehand) and sneaking past the bedroom window with a creepy, dissonant rising strings theme playing as she walks past. The mother may or may not open the window, adding to the tension. She also takes on an eerie shadowy look with glowing eyes, and will change into a demented-looking demon if she catches you. This all happens while the WarioWare microgames are playing on the Gamepad, adding dissonance to the situation.
Endless Ocean starts off as a fun little semi-educational game where you swim around the ocean and look and pet all kinds of fish. Then you start swimming in the deep parts of the ocean and encountering all the types of realistically detailed creatures that live down there. It's a bit surprising to go from swimming around a coral reef petting clownfish to swimming around a dark trench and running into a giant squid. In the sequel the last part of the story involves your fellow divers disappearing and when you find them being attacked by a giant deformed shark.
Pippin- The songs, the poster, even the characters will try and convince you this is a musical comedy "coming of age" tale. It's not.
A lot of Myst has this. Special mention goes to the brothers' rooms in the first game, and IV's Serenia - a lovely world of glowing butterflies, literal stone forests, and magic, memory storing lotuses. And then comes the Spirit Ceremony and the Big Bad's plan for Yeesha.
In Psychonauts, Milla's brain seems to contain nothing but fun and parties. However, if you manage to find a slightly out-of-the-way area, you discover that she used to work at an Orphanage of Love... which was destroyed and all the orphans killed in a house fire and continue to haunt her nightmares, crying out things like, "Save us, Milla," and "Milla, why won't you help us?" Reportedly, the original plan was to haveMilla's nightmares attack Raz, from time to time— this is where the Giant Space Flea from Nowhere mini-bosses in the Milkman Conspiracy stemmed from.
Ecco the Dolphin - A game starring a cute dolphin who has lost his family to extremely hungry aliens. He must go back and forth through time, battling past sharks, jellyfish, enormous spiders, and trilobites, braving eerie music and disturbingly solemn, frightened fellow dolphins, to rescue them and the Earth. Later locales include a meat grinder scrolling level where you're continually molested by terrifying masses of chitin and blobs of acidic green goo, and slime tubes in the sky that cause you to plummet five miles into roadpizza if you mess up and fall out. The final game in the series has you swim inside the body of a giant alien and attack its beating heart. Rated E for Everyone!
Aquaria follows a similar premise as Ecco, only this time the protagonist is a fish girl. She finds herself utterly alone and starts to explore the ruined civilizations, and eventually meets their crazy gods and the Big Bad who made them. And yes, just like in Ecco, there are Womb Levels in Aquaria.
Eversion starts out as a brightly-colored relentlessly cheerful platformer and ends as a Cosmic Horror Story, with the player character either being or being eaten by an Eldritch Abomination. Although if you know who H.P. Lovecraft is, the opening screen serves as a warning about that, as the game starts off by quoting him.
The game added its own Nightmare Fuel in form of the Heartless, creatures who, contrary to what their names imply, don't lack hearts; they ARE hearts corrupted by the darkness. These little monsters have one goal in mind: To corrupt all hearts that there are, and the hearts of the worlds they haunt are especially sought after. You know that the cheerful game those trailers announced isn't that cheerful when you see an innocent NPC being turned into one of those monsters as his face freezes in a fearful expression, and that's toward the beginning of the game.
"Miss World '96 Nude" is infamous as a horror game posing as a porn game. The gameplay consists of removing the obstructions that block your view of pictures of scantily-clad women. Take too long, and the image "turns" - the woman turns into a hideous monster as the gameplay gets harder. It's the ultimate in Fetish Retardant, and freaky.
40 Winks was intended to be a pseudo-nightmare played in a way that was positively adorable. Even though the "scary" aspects of the game were mild, the completely innocuous music and eerie simlish were complete Nightmare Fuel.
Ōkami: Most locations are vibrant with colorful characters, bright music, and thick-line artwork reminiscent of a Japanese scroll painting. The surprise comes mostly from two locations: the Sunken Ship and Yoshpet forest. They are creepy and quite jarring in contrast to the rest of the world. And there's also the Body Horror parts where you go inside someone's body, which is as nasty-looking as you'd expect (particularly the stomach acid dripping from the water dragon).
Free Realms: Merry Vale, the 24-hour party place where everyone has fun! ... too much fun to notice that their kids are getting abducted.
Hatoful Boyfriend: A very, very silly game about dating pigeons. At least until the backstory reveals itself.
Quest Fantasy is So Bad, It's Good, and involves characters who go "oh es so kawaii" and reference the zelda cd-i games. The second half of the game has characters dying and bleeding from their eyes and a boss that is a Shout-Out to Giygas.
Can Your Pet is a cute online Tamagotchi-style game in which you dress up, feed, bathe, and play with a baby chicken. Then you unlock the bicycle...
The webgame Cookie Clicker starts off mundane, then moves to ridiculous, then suddenly turns creepy when you unlock the "grandmapocalyse", with progressively warped images of grandmas appearing on the page background, creepy status/news updates that keep getting worse and worse from "unnerving" to "apocalyptic", and some disgusting worm-like things raiding your cookie stash, which you have to fend off.
Indie developer CC & SH loves this trope. It normally appears as an Easter Egg that you have to go and go very much out of your way to hunt down. For example, in their first ever game, Ping!, clicking specific spots on the screen during the end credits will cause the game to suddenly go full-screen, showing a black background with pulsating Chinese text and a very disturbing noise. You can't even exit the game at this point without bringing up task manager, either.
Calm Time starts relatively normal, with a party being held at a house in the countryside and the guests enjoying it and socializing. Then a girl in the kitchen asks you if you can hand her over the knife so she can cut the bread. Already from the way the main character holds the knife can you deduce that something is amiss, and shortly after that, shit getsreal.
The freeware game Dreaming Mary starts out, on the surface, in an adorable pastel-colored dream world where you play with a bunny, a penguin, a fox and a boar, fulfilling certain tasks from the first three animals and eventually getting all four seeds necessary to join the boar behind the last door. You're told through the radio that there are only three doors in the hallway, and you shouldn't look fora fourth one. Obviously, there IS a hidden fourth door, and entering it will unlock an alternate version of the dream world that can be entered through the painting in your bedroom... It's a shadowy, Real Is Brown, blood-stained living room with the plushies that three of the dream animals represent (each getting torn up after receiving a seed) and the stuffed head of a boar, and it's all pivotal to unlocking the Golden Ending. Also, watch out for the crude shadowy figure that chases after you whilst calling you a "sweet girl" in its deep, uncanny voice.
Monster Pulse: It's all fun and games until someone gets their head bashed in with a rock. Although the entire premise of "organs being ripped from the body and turning into giant monsters" might also fit the bill.
Issues 8 and 10 of Sonichu. The former explores the titular species' sexuality in disturbing detail, and the latter has Author Avatar Chris-Chan eliminating everything he hates, from homosexuality to Encyclopedia Dramatica and 4chan (represented by Chris destroying an entire building full of people), and finally brutally murdering the four people behind Asperchujust for making fun of him. All in a webcomic supposedly meant for children.
Quite a few series in The Slender Man Mythos use this trope. Several start out as ordinary video or web blogs that seem perfectly normal for the first few entries, only for things to go creepy when Tall Dark And Faceless pops up.
Tokyo Magic Star starts out as a normal magical girl fanime. Things go downhill from there.
Courage the Cowardly Dog, taking cartoony premises and villains and making them genuinely horrifying. Katz is probably the most frequent source, as when his latest overly elaborate Death Trap fails he usually just resorts to strangling Courage.
The original My Little Pony pilot, "Rescue at Midnight Castle". Starts off with rainbow ponies playing around and a cute song, and then suddenly switches to ponies being kidnapped by the dragon-like minions of a demonic centaur. It only gets worse after that with the ponies being turned into monsters, and the villain threatening to decapitate a baby dragon.
"Lesson Zero", infamously so. The series is no stranger to Sanity Slippages, but Twilight's descent into paranoia and insanity, complete with an endless parade of Nightmare Faces, is immensely disturbing. "HIII, GIIIIIRRLS!" indeed.
In "Hearth's Warming Eve'', the play starts out somewhat serious, but still not that bad. Cue Eldritch Abominations feeding off the founders' Fantastic Racism and attempting to freeze the entire world. Keep in mind that the play is based directly off of the history of Equestria's founding, so it most certainly did happen in "real life".
"Baby Cakes": Aww, it's a babysitting episode, how kyuuute! Wait, where'd they go, and what's with the sinister music?
"A Canterlot Wedding:" Twilight Sparkle has apparently messed up big time, and she's sad, but it looks like Cadance and she will make up. Then HOLY HORSEAPPLES "Cadence" is evil! Part 2 ratchets up the horror even further, with a full scale invasion of Canterlot by bug-like shape-shifting monsters.
The Chimera from the episode "Somepony To Watch Over Me" in season 4 was definitely a big surprise. She is arguably the creepiest villain in the whole show, and is especially surprising because it is the first time a truly scary villain has ever shown up in any episode that wasn't either a season opener or a season finale, and that episode seemed like a typical comedic Slice of Life episode at first.
Sweetie Bell's nightmare in "For Whom the Sweetie Bell Toils" is surprisingly disturbing for an otherwise mundane Slice of Life episode.
Rango starts out as a fairly light-hearted Western for kids, with only a few sinister villains to occasionally darken the skies. Then Rattlesnake Jake shows up, and introduces us to a new meaning of fear.
"Holly Jolly Secrets" is by far the most infamous example. A two-part episode composed mostly of Christmas-like hijinks and watching Ice King's embarrassing video diaries, it ends with the most shocking and depressing reveal in the entire series, forever changing the nature of a main character. "My name is Simon Petrikov."
"Beautopia" is nowhere near as bad, but when those inflatable pool floaties turn out to be anything but, even the characters are terrified.
"Finn the Human"/"Jake the Dog" begins in an Alternate Universe where Finn is a normal kid with a normal dog and deals with normal family problems, trying to help his parents with a gang of thugs. Cue the Destiny Gang burning down Finn's house with his family still inside, Finn becoming the Ice King and losing it in a horrifying way, and the origin of the Lich.
As the picture shows, a short called "The Snowman". Starts off really cutesy, with a human and his animal friends building a snowman and dancing around, but all hell breaks loose when the snowman comes to life and goes on a rampage.
By the same company, "Circus Capers", a cartoon that blatantly plagiarizes the designs of Mickey and Minnie Mouse, starts off pretty generic and happy... then Minnie is revealed to be cheating on Mickey with the obvious villain of the cartoon. Mickey discovers this, and almost instantly becomes fat and depressed. He begins to sing "laugh clown, laugh" with a horridly wrinkled and disfigured face. In response, Minnie realizes her horrid mistake, attempting to return to Mickey. He rejects her, and, out of nowhere, HIS FACE COMES OFF OF HIS BODY, ENLARGES, WINKS AT THE SCREEN, AND INFLATES, COVERING THE ENTIRE SCREEN WITH THE BLACKNESS OF HIS NOSE. What follows in several prints of the cartoon is a quick cut to a bunch of happy dancing ducks from the unrelated short The Booze Hangs High. A couple prints give a "The End" screen instead of said ducks, but one wonders if that wasn't the actual ending.
The Phineas and Ferb episode "Phineas and Ferb Get Busted!" starts as a typical episode, but it all changed when their mother actually finds out about the boys shenanigans. From then on, it becomes way darker and morbid than a typical episode. It turned out to be All Just a Dream at the end, but still.