When I saw this thread title, the first film that came to mind was Jurassic Park. Glad to know I'm not the only one. The book is terrible.
Another big one for me--and I know I'm committing heresy by saying this on a comic book forum--is Watchmen. Zack Snyder's film completely transcended the graphic novel IMO, in particular by changing the novel's offbeat (read: WTF?) climax.