Two of my most memorable experiences whilst watching a horror movie in a theatre:
Inappropriate and not funny.
28 Weeks Later  - Definitely one of my favorite horror films owing to the fact that the fear stuck with me for quite a while after. The inappropriate reaction came during an extended chase scene midway through the movie. The big bad military chases the main characters who flee in an old sedan. They elude the foot and car patrols but then a fully armed attack helicopter rises up from behind a building and begins firing rockets. At which point I burst out laughing. I can explain though. This time (just this once) I was not, in fact, hoping the protagonists got killed. It was just that they just had all this might coming down on them it was ridiculous.
Appropriate but funny.
Quarantine  - Drawing close to the end of this film, the black guy from The Practice pokes his camera up into the attic to do some reconnaissance. After about 340º of rotation a child-like pseudo-zombie screech-and-lunges at the camera. The best part was this: there were 4 black peeps sitting a few rows ahead of me, arranged like so:
At the screech-and-lunge Person #1 yelped, jumped across 2 seats and landed in Person #4's lap. AHAHAHA WHAT A WANKER.