Though I ultimately didn't like the movie, I thought the "bite the pavement" scene in American History X was kind of creepy.
I squirmed a lot during the "drug the family" scene in Happiness, too.
...then there's The Accused...
What's funny is the movies & genres that specialize in making you uncomfortable usually don't faze me.
There are to scenes that freaked me out because I didn't notice the freakiness the first time I saw them. The movies are The Virgi Suicides & Carrie
SPOILERS!!!
I mentioned The Virgin Suicides recently. At the end of the movie where the four sisters kill themselves, one of them is hanging in the basement where, a year earlier, a party was thrown for the youngest sister, Cecilia. Cecilia already tried to kill herself once, and the party was supposed to be a way for her to meet other people her own age. During the party, Cecilia went upstairs and threw herself on the iron gate, impaling herself. At the end of the movie, in the basement, we see that all the party decorations are still up. The balloons are deflated, and things are in disarray, but nobody thought to take down the decorations from the first suicide, almost a year earlier.
In Carrie, near the end, Carrie gets home after the Prom Night From Hell. She's in shock, covered in blood, and searching for her momma. What she doesn't know is that her momma has truly gone off the deep end. The camera is following Carrie, framing her back, as she walks from one room which is dark, to the bathroom to wash up. When she turns on the ligh in the bathroom, we're still in the dark room, I think it's her bedroom. The light from the bathrooms shines through the gap in the door, ansd we can see Carrie's Mom, Piper Laurie, on the other side, with a look on her face like an old Death Masque. It's disturbing enough as it is, but since I didn't notice it the first time, I was wholly unprepared for it. You know when you see a horror movie twice, you always assume you'll be OK, because you know where the scary shit exists? That was me...until that scene.