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The ghost of the dead cyclist appearing next to Cole's car window, especially with how the shot just comes out of nowhere.
Ghosts aside, the opening scene with Vincent is scary. We have a mentally unstable man who breaks into the house of his former psychiatrist. Said psychiatrist tries to calm him and gets shot for his trouble. This scene gets special mention because a situation like that can likely happen.
The twist at the end can be considered this too. Malcolm is a character we've gotten to know and even care about. And the fact that he's been dead this whole time is honestly startling to see. The music and accompanying scenes add to the creep factor.
The woman who slit her wrists screaming at Cole when he sees her in his kitchen. Also doubles as a Tear Jerker.
"YOU'RE A TERRIBLE HUSBAND, LENNY! LOOK WHAT YOU MADE ME DO!!"
Cole seeing the people who were hanged in the halls of his school.