My vote goes for Tomb Raider II and the floating islands levels. The game is a relativity normal globe trotting affair for Lara until she gets transported into the fucking shadow realm here. This level gave me major scares as a kid since you're traversing a giant void being chased by animated statue warriors out to kill you.
The Marathon trilogy, a 90s bungie FPS with, notably for its time, a story. Bizarre, frightening creatures sneaking up on you throughout, in dark spaceship corridors and ruined alien castles. It has clear inspiration from the movie Alien, but plays more as action/puzzle than survival horror.