I can't believe nobody's mentioned 2001: A Space Odyssey yet. I have yet to meet somebody who thinks that movie is "okay" or "all right"; they either think it's a cinematic masterpiece too good for words, or a mind-numbingly boring and pretentious collection of tableaux. I fall in the first camp, but know many more who hate it.
Ditto for Napoleon Dynamite; I think Kevin Smith's movies also appeal to a small, select crowd rather than the masses. I remember that the reaction to Pulp Fiction was rather mixed as well when it came out, due to its novel time organization format, and I still know people who think it's too disjointed. I personally liked the movie, but thought it was much ado about nothing, and hardly a masterpiece (I know 2/3 of BL will hate me forever for writing that).