Wow, I'm surprised to see so much "2001" hate around here. Whenever I tell people that I think Emperor Kubrick isn't wearing any clothes -- at least when it comes to that film -- they look at me like I'm insane. Honestly, though, aside from the HAL business and a few arresting visual moments, "2001" strikes me as the epitome of boring, pretentious art-film wankery. If it weren't for the accompanying music, the giant space fetus at the end would elicit more guffaws than anything from the Star Wars prequels.
Others:
The Thin Red Line - actually, THIS is the epitome of boring, pretentious art-film wankery.
Donnie Darko - I'd probably slap this with the BPAFW label too, but the creepy bunny is at least some fun.
The Searchers - I've never been able to get interested in the folksy, sanitized Westerns of the John Ford era. This one gets extra demerits for trying to say something serious and failing. When you cast artificially tanned white people as Native Americans instead of, you know, ACTUAL NATIVE AMERICANS, your condemnations of racism tend to ring rather hollow.
Superman - hasn't aged well.
Snow White and the Seven Dwarves - ditto.
Primer - I can appreciate what they were trying to do, but this is that rare instance of a low budget seriously hampering my enjoyment of the film.
Ferris Bueller's Day Off - All I can say is, I want to slug Ferris Bueller right in his smirky, platitude-spewing mouth.