This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Witch's House
Cutting the limbs off a teddy bear and having the stumps bleed like a living creature is pretty creepy. Not to mention what happens shortly afterwards when the bear gets its revenge...
Early on, Viola finds a kitchen where an invisible chef is working. He/she takes Viola's offer of 'a hand' a bit too literally and then presumably hacks the rest of her to bits too.
It gets worse. Later she can go through an adjoining door into the pantry. A pantry full of human skeletons, none of which have hands...
Many of the potential deaths that can claim the player count. Whether it's being eaten by a giant snake, trapped in a tiny room and crushed to death by a giant boulder, decapitated by a giant spider...
The house and its inhabitants tend to move around a lot, often just out of the player's field of vision or when Viola leaves or enters a room. Creepy every time it happens.
The new ending, "____" depicts what would have happened if Ellen, as Viola, never entered the house. If you think the state that Ellen's body was in, it would only be a matter of time before Viola dies, which explains why the roses wilts away. But remember that triggering this ending requires a lot of time. Imagine how much Viola would have suffered, having her eyes gouged out, her limbs cut off, and her voice rendered unusable, and her only chance of fixing her situation is ruined because Ellen never walks back into the house, waiting each agonizing minute before perishing. This is Fridge Horror at its finest.
The fragments of the witch's diary scattered throughout the house are pretty chilling.
The dark maze on the top floor is scary enough on its own (especially when you start hearing the statues moving around), then you drop and break your only light. Word of advice: do not pause the game at this point.
Despite being so laden with Paranoia Fuel, there's actually only one thing that's really dangerous in the dark maze: a watch you can pick up. You could miss it in there certainly; but if you do run into it, considering that you're already conditioned to pick up everything you see in this game, you'll almost certainly take this watch too. If you pause the game at this point you'll see the same Nightmare Face as in total darkness, and the description of the watch simply says "DIE". After you take a few steps, a rope or tentacle will come out of the ceiling to hang Viola.
YMMV, if you did not use the save points at all. The cat will reveal he is a demon and calls you Ellen, not Viola. At that point, you WANT her to catch you, as you know thats the only way to a good, if unofficial, ending - except it isn't since the body-swap requires trust and willingness, something Ellen-as-Viola doesn't have at this point.
Just the whole idea of being trapped in a house where everything's trying to kill you with no way out and no way forward but towards the one who presumably created and controls it all.
The novel reveals that all the monsters in the house, are people killed by Ellen in the past. Since Ellen in Viola's body is powerless now, it's no surprise that the monsters want their revenge.
Ellen tricking Viola into entering a mutilated body.
The player learning the truth of Viola and Ellen. The Ellen that has been chasing after the player is really Viola trying to get her body back and return to her normal life. The player unknowingly helps Ellen in Viola's body escape the house and unintentionally cause her death.
The true end is pretty much any parent's worst nightmare come true. Not only do their child associate with someone responsible for multiple disappearances, but they also get used and betrayed by someone they once called a friend. It's even worse when Viola's father shoots Viola in Ellen's body, thinking that he's protecting his daughter. This is sure to make people question who they should trust.
When you feed your frog friend to the giant snake in order to save your own skin and then pass through the room where the snake formerly was, at the last second as you open the door to the next room the frog's ghost will appear behind you. If, after entering the next room, you immediately go back into the room to check out what you just saw, the entire room will have transformed into a nightmarish scene, with ghastly sounds and a floor that looks like a nightmarish pool of glowing blood and gore. But then if you leave the room again, everything in it is totally back to normal throughout the rest of the game; the brief transformation never affects any other part of the game, and the character never comments or reflects on it. It's as if it never happened, somehow making the fact that it did happen all the creepier.