The puzzle with the painting of Stauf's face. The character is creepy enough to begin with (he's an insane toymaker/millionaire who opens the game's intro sequence by murdering an elderly woman for her purse), but in order to solve the puzzle, you have to cycle through bits of his face that look like lizard skin or demon skin (complete with horns), and when you finally finish it, it looks like Stauf is trying to bite through the painting and attack you).
The fact that you find yourself looking out through the main character's eyes, with no idea what you look like, or why you're in Stauf's mansion, or what the hell the other six people who entered the mansion hard on your heels are doing there.
Coming across a boy in the mansion, and, unless you've done some very thorough searching on the first floor, having no idea who he is or how he entered the place.
That damn creepy children's rhyme that plays after you finish the puzzle in the library. The developers knew they had a winner on their hands with that one - it's the only scene involving the tragic/comic mask cursor that can be replayed more than once.
The woman in the white dress who floats around the second floor hallway. Even after playing through the sequel, we still have no idea who she is or what she's doing there. (Maybe Stauf had a wife - which is Nightmare Fuel in its own right.)
Stauf screaming "COME BAAAAAAAAAACK!" when you quit the game.
The Freemason-style pyramid cursor, with that single eye staring at you. Also, for that matter, the throbbing brain cursor. In fact, even the standard skeletal hand was pretty damn creepy when you consider that it was the default cursor. And this was back when most of us were used to seeing the nice, ordinary hand cursor in Myst.
The labyrinth appears to have been designed to maximize paranoia and Claustrophobia. There are two main structural elements of which The Maze is composed: compact, twisting corridors designed to disorient the player, and long, straight corridors designed to make the player lose track of their position in the maze. All the paths except the one that leads the exit lead to dead ends, and every time you hit one (which you can only see when you've reached it), a Scare Chord plays and Stauf would inquire, "Feeling...lonely?"
Also, can't forget the scene after solving the dollhouse, when you learn that the dolls have children's spirits inside. The game's intro, which tells the tale of dolls killing children through illness, was scary enough without all that.
Hell, what about the scene that plays before that, with all the toys flailing and crying as you enter the room?
The painting at the top of the staircase? When you click on it, you see the shape of hands outlined and pushing/distorting the painting in all directions, as if someone was trying to escape from inside the painting, before it finally snaps back to looking normal.
It also may remind some people of Freddy Krueger trying to get to you.
Many things in the original script didn't make the final cut, probably due to the technology of the time.
One of the more particularly jarring ones is an animation that would have been activated after solving the Front Door puzzle. If Ego opens it and steps through, he only ends up back in the foyer again, facing towards the stairs.
Consequently, some of those unused scenes contained explanations for Stauf's real plot.
A nursery scene that was cut:
-A top spins, creating an eerie WHISTLE that turns into the screaming of dozens of children.
What about the scene after the tile puzzle in the Chapel is solved? The altar is draped with a red carpet, and besides Stauf dressed in robes talking to Brian Dutton, there's a baby writhing and crying on the altar, and when you consider Stauf is telling Dutton that he needs a living sacrifice, well...
Stauf: Now! Now the sacrifice must come from you. *cackle* It must be brought to me... ALIVE! A final... sacrifice!
It gets worse if you've read the script or the novel. There were meant to be more people in robes holding the baby down on all sides.
The 11th Hour
The Marie ending.
"How about...a Chuck roast?" The capitalization there is not a typo.
How about a freaking tiger advancing on Robin during a cutscene?
How about a flashback wherein Marie's mother, Eileen, is running away from Stauf's mansion, gets her hand stuck between the bars of the locked gate... and screams bloody murder while the gate eats her hand clean off?
Or slightly later in that video where Eileen is at the doctor's screaming, and raises her arm, you can see the ragged stump, with twitching bits of sinew/muscle and blood running out the artery.
The 13th Doll
How about the entire premise? Poor Tad (you know, Ego) never got over what happened to him in the first game. He's locked up. And now his brilliant new doctor decides that the best way to help him get past his so-called delusions of what he suffered is to go back to Stauf's mansion and see once and for all that it's not real. Except that yes, it is.