Here's mine separated into two categories of why they're hard to watch (under the spoiler alert since it's a bit long).
Hard to watch because they're bad:
BloodRayne- I had endeavored never to watch that piece of crap, but then decided "why not" when during my lunch break at work (my coworkers liked occasionally having "Bad Movie Lunch"). Truthfully, I dislike Uwe Boll in general (more for his shitty attitude than his reputation of terrible movies) but this is the only one I've actually watched instead of seeing clips/reviews and it was as terrible as everyone lets on. The dungeon sex scene was particularly awkward to sit through and literally came out of nowhere as far as I could tell.
Paul Blart Mall Cop- I really dislike this movie and part of the reason, other than it genuinely not funny, was the marketing. The tone wasn't at all right in the ads. It looked like it would just be a silly romp about a dogged but ineffective mall cop that saves the day (not the best premise, but it could have its moments of comedy), instead it was much less light-hearted story about a mall cop that's a total loser who gets stepped on all the time that admittedly still got to save the day.
Twilight- Another one from "Bad Movie Lunch." It was actually one of the ones later in the series, maybe New Moon but I'm not entirely sure. Either way, I didn't much care for it. All of the characters are so dull, particularly Bella. It would be way too much work to list all of the problems I had with this movie; it's just not a story I'm into.
Hard to watch, but I still like/respect them:
Grave of the Fireflies- Ever want to see a soul-crushingly depressing movie? Here it is. I knew it would be depressing before I even watched it (because of the synopsis) but it was rated 3+ if I remember right (or maybe 7+, it was something for very young ages), which most certainly happened only because it's animated. I can tell you that's definitely the case because it's of two kids that become orphans because of some firebombing on Japan during WWII... and then it got worse.
SPOILER
Both of them die. Setsuko, the younger sister who was 3-5 years old at most, dies of starvation right when Seita, her old brother and the main character, finally brings back food. So then he cremates her remains and gives up on life and dies, too. Also, some time around that cremation scene I mentioned, there's a montage of Setsuko being adorable while the song "Home Sweet Home" plays.
/SPOILER
It's extremely difficult to watch. I still don't have it in me to watch it a second time.
2001: A Space Odyssey- The only part of this film I really enjoyed were the bits with HAL 9000 in it. The rest of the movie was ponderously slow (like the primates with the monolith) and seemed pretentious (the star-child ending).
Pan's Labyrinth- It's just a difficult movie to watch since it has such an oppressive tone (though that seems to be part of the point). The guy getting his face beaten in with a bottle was particularly hard to watch; I tend to dislike scenes of torture or curb-stomp type beatdowns.
Watchmen- It was a good movie, but some of the stuff in it is just unpleasant. I also didn't like Silk Spectre and Nite Owl's awkward sex scene together; I have a dislike for awkward sex scenes in general, but that one was especially painful. Showing them nude while grinding slowly on the wrong spots for practically 5 minutes and playing the song "Hallelujah"? Ew, no thanks. That scene was like, what, 3 panels in the comic? And Alan Moore's certainly not one to shy away from nudity or sex scenes.
I don't even know where to put The Room (which was so bad it's funny). Admittedly, I've only seen the full movie on Adult Swim, since I had never gotten to renting it before then but I seriously doubt I'd find it as easy to watch it otherwise. I don't think the sex scenes were as bad as Adult Swim acted, censoring large chunks of the screen during them (it was April 1st when they played it), but I really don't want to see Tommy Wiseau awkwardly having sex.