I just bought Akira on DVD, you know. Looking forward to another hour or two of mindfuckery broken up briefly by "TETSUOOO" and "KANEDAAAA."
I think I've been ninja'd a few times, but my answer is Assassin's Creed 1 and 2. The first pretty much came out of nowhere and went Lost on otherwise forgiveable levels of stupid, the second said "screw it" decided to elevate that to the level of "batshit insane." Prince of Persia got a similar treatment, thus I have reached the conclusion that whoever is making these plots needs to learn how to make a satisfying ending. You don't need to disrespect your audience so thoroughly to make an ending that allows for a sequel.
Pretty much all of my favourite films have a mindfuck in there somewhere, usually culminating in the last half hour or so (Hell, I'm an Assassin's Creed fan still.) Donnie Darko is an obvious one. A far less known one is probably the film adaption of Neo-Human Casshan, Casshern, which I needed to Google a proper explanation of. I think it relies a bit too much on Japanese cultural knowledge or an audience used to this sort of plot (it reminds me a lot of Akira in that way) because I just did not get a lot of the plot. However, it has a fight scene where a guy destroys a legion of giant robots with his bare hands, and is therefore excused. Also messages about mortality, racism, politics... but he does karate chop a robot in half.