Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
Nightmare Fuel: The Secret World
Amongst other things, the Dimir family. The farm where they live and work is creepy enough, what with all the dying vegetation and the angry guard dogs roaming around; then it turns out that most of the sausages hanging in the abattoir are actually ghoul meat- to say nothing of the innocent gnomes and fairies that have been made into stews here.
Silviu and Olga are terrifying in their own right: Silviu because he's a Psychopathic Manchild with an addiction to murder and a habit of chanting insanely to himself; the only thing stopping him from killing you and making you into sausages is Olga's command. The moment where he first looks up from hacking up a dead ghoul and sees you is just chilling. On the other hand, Olga's just as creepy, given that she's a vicious old bitch who controls Silviu's every move and every aspect of the butchering operations. The little speech she makes doesn't help.
You cannot wash your hands of us; you need us! Your world needs us to do what you cannot do! You need us!
And then, in the mission following this, you venture into the Dimirs' basement: it turns out to be an abandoned Soviet bunker, used to house all the magical creatures that the Dimirs capture before they're finally slaughtered and eaten. Most of them are ghouls, but at least one was an innocent satyr. Worse still, in the Dragon ending to this mission, it's implied that Silviu spent time down here as a child, getting a taste for murder- possibly while imprisoned in the same cells as his ghoul victims.
The Black House. Subverted in that it is one of the easiest early missions to grind for XP on the account of there being no monsters to fight. Then again, there are no monsters to fight, just the house itself...
And then, The Reveal. The Black House isn't evil, just very, very angry at the fact that the townspeople vilified it and its owner, who was honestly a good person.
The Filth. Not the material itself; black eldritch goo is rather trite in these settings, and tentacles are meh. But what it does to the contaminated? How they scream and cry for you, stop stop they can't stop, please stop stop me? Or that underneath, in areas and lands where the world and reality itself has been blasted away by the stuff, underneath it all, we are made of stars?
"The Vanishing of Tyler Freeborn." Protected only by a gas mask, you finally get to see what's behind the Fog; once you follow the siren song past the thick banks of clouds, it turns out to be a pocket dimension owned by the Dreamers, where Kingsmouth has been rebuilt as a twisted World of Chaos-style parody of itself, with endless picket fences, ominously crooked houses, roads covered in sprouting Filth tendrils, a sea of wrecked ships floating in a sea of Filth, and all of it beneath a pitch-black sky. It's inhabited by Filth-infected duplicates of the Kingsmouth townsfolk, all of whom try to kill you on sight- because their real-world counterparts have received mild infections and are due to become Filth creatures in the near future. Worse still, there's no way to stop the Dreamers in this mission; the only thing you get out of the entire quest is the knowledge that Tyler Freeborn died trying to escape the Fog.
"A Dream To Kill." Your Faux Action Girl companion turns on you, knocks you out, straps you to a table, reveals herself as the Big Bad, and then cuts off your legs.
The notes of Doctor Schreber includes several disturbing notes and headers, the least of which is probably "Methodologies for opening the Event Horizon of Endless Hunger in the chest cavity." Incidentally, the information contained behind that header has been mercifully deleted. On top of the terrors unleashed by the Orochi Group's groundbreaking investigations into lycanthropy, ghosts, fungal infestations and even anima-infusion, the really disturbing thing about this is that Schreber found possible applications for them: were-creatures able to transform into anything, ghost-induced intangibility, even mass-produced versions of the player characters. For an final dose of of horror and disgust, realize that all of the human test subjects used in these experiments were children.
The Nursery. The overly-colourful scenery, the creepy "lullaby," the robotic nannies that speak in calm, mothering tones and try to kill you if you turn the music off... and that one room where you can find a bloodied corpse lying at the centre of a huge crowd of naked dolls.
Emma's past; the few details you've been able to glean from the Smith's computer and other earlier missions are creepy enough... but things get unnervingly surreal when you start exploring her memories from her perspective and enter her recollection of the burning house; because she was only a small child at the time, the world seems to grow around you until you're dwarfed by the kitchen table, and the upstairs corridors seems to go on for miles.
The Filth takes on another disturbing aspect in this recent update: it's infected Agartha. And by the end of this issue, the tendrils are still there, still growing.
The conclusion of the issue: Emma manages to temporarily defeat Lilith... only to end up face to face with a gang of Filth-monsters, all of them whispering her real name; for perhaps the first time in the entire game, Emma is almost paralyzed with terror - not of the monsters, but of what's controlling them.
What do you want? I'm so small... you eat stars...
You are all made of stars...
Quite a few of the Spooky Stories of Solomon Island from Halloween 2013:
The Rogue Groundskeeper: Innsmouth Academy had a groundskeeper that spied on several students, caused several "accidents" resulting in grievous injuries, and killed three seniors who tried to rat him out - perceived as suicides by the teachers. And when other kids tried to discuss their concerns with Montag (this time at a school assembly), it turned out that the Academy hasn't had a groundskeeper since 1806.
The Phantom Email: Spam emails aren't just examples of annoying junk mail - they're actually messages from a rogue AI haunting the internet, trying to perpetuate the existence of the characters of each email and getting angrier and angrier as it's pleas for attention are ignored. And those chain letters that threaten you with death or injury if you don't continue the chain? The entity sometimes makes good on those threats. Even worse, the man who found and printed out this email for you to find was none other than Tyler Freeborn, and did this two days before he made his fatal journey into the Fog.
The Lantern Man: A young woman engaged to the man of her dreams unexpectedly contracts smallpox, and though she survived, she was left with permanent scarring. Desperate for a means of recovering her lost beauty, she ultimately went to a Wabankai shaman for help, and was given an ointment that would apparently make her skin smooth again. Unfortunately, the shaman was still in mourning for the members of his family who'd been killed by the same plague, and didn't appreciate being bothered on such a trivial matter; the ointment didsmooth out the young woman's skin... to the point that it melted right off. The "cure" was actually sulphuric acid.
The Death of Dr Armitage: The description of the Doctor himself; plus, the fact that there's a Filth-infected occultist wandering the world, searching for writers who are willing to perpetuate his existence in their work in exchange for success. And the story also claims that, if you fancy yourself a writer, you might be visited by him one of these days.
The Fear Nothing Foundation in Tokyo. Combines the psychological abuses and practices of real cults with supernatural elements. In addition, one of their members caused the massive filth release in Tokyo that started the events of the game.
On a related note: Every time a person goes through a tutorial mission, viewing the Tokyo Incident Team's disastrous scouting mission, they are unknowingly becoming an accomplice to repeated Mind Rape of the member who got stuck in the subway. And it's going to keep happening, because your society doesn't know any other way to prepare operatives for the Filth safely.