There's actually a website that deals with this sort of thing. Let me look it up and I'll get back to you.

Harry Potter and the Philosopher's/Sorceror's Stone - Professor Quirrel is Voldemort's helper; Snape is innocent.

Harry Potter and the Chamber of Secrets - Ginny was used by Tom to attack and vandalize Hogwarts. Lockhart is a fraud. (though that's kinda obvious)

Harry Potter and the Prisoner of Azkaban - Sirius is innocent, and he is also Harry's godfather. Peter Pettigrew is the traitor. Remus Lupin is a werewolf. Sirius, Remus, and Peter were friends of James's, Harry's dad.

Harry Potter and the Goblet of Fire - Cedric dies. (I think someone else dies too but I can't remember who) Professor Moody is really Barty Crouch Jr and it was he that put Harry's name in the goblet.

Harry Potter and the Order Of The Phoenix - Sirius dies. That's about 2 years already, but people are still touchy about it. (and I think this is the most memorable spoiler from the HP series so far.)

Memento was pretty mindboggling. Sammy Jenkins was actually a con artist. It was Leonard who killed his wife with insulin injections. The supposed "killer" had already been killed; Natalie was using Leonard to get back at Jimmy Grantz, a drug dealer (and her ex, I think) by manipulating his weakness. Leonard willingly chooses to forget Teddy's murder, and goes out in a search for another JG.

Vertigo - Judy Barton was hired to act as Madeline; the real Madeline had already been "dealt with" (killed?) by the husband.