schindler's list and saving private ryan probably effected me the most physically, viscerally, especially the latter--i saw it in the theatre with a friend and i think we were actually in shock from that one, i remember walking home and we were both so floored by what we had seen it was like we were in a daze, neither one of us spoke on the way home. it was really powerful. schindler's list was even harder to watch, though i saw it at home on video. that one physically hurt to watch. so much suffering, so much cruelty--i can't watch movies like that more than once or twice in a lifetime. too hard.
some others i found emotionally powerful were waking life, the science of sleep, taxi driver, LOTR trilogy simply for the pure joy of seeing the books i love so much transformed into film, blindness, bobby (about RFK), donnie darko, almost famous, the deer hunter, the wall, the wind that shakes the barley.....there's just too many, i love cinema and i watch a LOT of movies each year lol
oh yeah, some great funny movies i've seen are rushmore, superbad, anchorman (i know, but sometimes i can't resist silly), obviously the holy grail the life of brian and the meaning of life all by monty python (quite silly ), zoolander.....once again, just too many to list, but that's a start anyway.