Someone has already mentioned eyes, and that sort of thing I don't like, but if it's done "Correctly", I'll actually want to cover my own eyes, case in point: "A Serbian Film" and "Eastern Promises".
"A Serbian Film" is awful, disgusting and above all else, something I'm glad I cannot defend anymore, because I slowly realized the movie served no purpose to explain Serbia itself, but instead aimed to elevate the squick factor to be over the top and horrifying. There isn't a scene with an eye, per se, but a socket on the other hand... I actually covered my eyes, a practice I don't do at movies much anymore.
"Eastern Promises" has an eye scene that's actually hard to watch, but it's the follow up from a badass fight sequence, which is still of one of my favorite fight scenes in movies to date, so it seems fitting, then.
Things that make me cringe in media:
- Bad Singing. This is usually lumped together with bad acting in the same scenes, so you have somebody deliberately doing a bad job of both performing and singing the lyrics to some song, and it just makes me uncomfortable.
- Bodily humor, especially when it's just crammed in for no reason. If you have to make a fart or period or puke joke, even if nobody is in the room, I begin to question why the movie was made, and for that matter, why am I watching it? If it's something in a context where it makes sense (Blazing Saddles does it excellently, or Airplane! for the one time it does it because it's meant to parody, even Dumb and Dumber did it well enough by only doing it once) that's fine. They are all normal functions, I understand, and some people have adverse reactions to things, but if somebody has to cut one and it feels forced.... Please stop it (Eugene Levy and Samuel L. Jackson were in a movie called "The Man", where it felt forced, and the movie was torture to begin with).
- Characters who call other characters something that's not really an insult would count as one. I don't know why, but hearing the Green Goblin in the 2002 "Spider-Man" called J. Jonah Jameson "Slime" always makes me slide down in my seat. It's just so silly, it makes me cringe. If you are going to insult somebody, you can find better ways to call somebody something unfavorable.