Jacob's Ladder, Flatliners, Stephen King's IT miniseries and parts of Tales from the Darkside: The Movie (The Lover's Vow segment) all scared out of me when I was growing up in the 90s. The opening intro theme from Tales of the Darkside television show was pretty freakin' scary as well.
Honorable mentions for great 90s horror movies were Event Horizons and Stir of Echoes.