Ton's of shit comes to mind... Fight Club can definitely be up there in the list. Gotta hand some love to Primer, granted I know a lot of people really didn't like it. Fuck them. Same with Vanilla Sky. Jacob's Ladder (Tim Robbins best movie still). The Shining was also a pretty good mindfuck. Along with A Clockwork Orange and 2001... Kubrick was a great mind-fucker. Then there's stuff like Cube, Total Recall, Twelve Monkeys, The Matrix (ignoring the fact there sequels may or may not have been made), and Dark City.
Mind fucks, fuck yeah.