Strangely enough, the newer movies simply don't scare or disturb me anymore. That's probably the result of almost 40 years of desensitization. But there are some scenes from older, 1970s Italian horror movies that made me somewhat queasy:
1) City of the Living Dead: The scene where the girl and her boyfriend are in his pickup truck, and the evil dude blocks their path. She's staring at him, and slowly blood starts coming out of her tear ducts. It starts pouring faster and faster, until she starts throwing up all of her internal organs in one continuous stream. The effects were particularly effective for such an older movie.
2) The Beyond: There's a scene where a guy falls off a ladder and is lying on the ground, pretty much paralyzed. A bunch of tarantulas come out of the woodwork, crawl over to him and slowly start eating his face, starting with one that enters his mouth and begins eating its way outward. The effects are beyond laughable but there's just something about the music in that scene that bothers me to this day.
The only modern movie that gave me any kind of chills is Event Horizon. When you finally see what's on the grainy video and how it ties in with the audio recordings you'd been hearing bits of throughout the movie, it's pretty freakin' nasty.