Watchmen. It's not a bad film by no means, I'll say right now. However, there were so many things that were either left out, modified , or, in the case of the ending, totally changed that it just annoyed me in numerous ways. Plus, the amount of blood splatter was far too over the top when compared to the book, and the almost pornographic sex scene in the movie wasn't nearly as explicit in the book either (and trust me, I'm not the type to usually complain about too much blood or sex!).
It was a pretty good film on its own right, but as an adaptation of the fantastic graphic novel it was severely lacking.
EDIT: Oh, and the film version of "To Kill a Mockingbird" annoyed me as well. Say whatever you like, that the film was a great portrayal of an important event from a child's eyes and the like. The fact that various characters that were truly important to the theme of the book were axed in the film, and that the book's ending monologue, which left me stunned after reading it, was reduced to nothing more than a single line in the film that totally ignored the main point of the book monologue pissed me off like you wouldn't believe.
In my opinion, "To Kill a Mockingbird" is one of the most overrated book adaptations I have ever seen, and is nowhere near as excellent or moving as the book was.