This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / the white chamber
The scene when your character faces the monster on the station rotation control, or the scene with the eyeball in the extended hallway to the cradle.
Thankfully, there's only four actual ways to die (the mandatory one doesn't count), and all of them can only be done if you choose to get said endings, or if you're impossibly stupid.
The worst ending. As with the standard failure ending, you find yourself back in the coffin. Then disembodied hands reach out of the darkness towards you. The ending being still images instead of animated does not help. It's quite frightening.
And right after that, they start tearing you apart.
Never, ever listen to the soundtrack unless you are actually playing the game. If you listen to it at any other time, whatever you are doing at that time will be ruined.
One of the Dark World sequences involves part of the ship leading back to the control room turning into a deranged maze straight out of Hell, complete with blood stained everythings, suspended torsos, and pulsating eyeballs.
The fact that Sarah, the cute girl you play as, is responsible for the horrible deaths of her fellow scientists, which include throwing one into an industrial fan, gouging one's eyes out, cutting them apart, etc.