I personally like both the graphic novel and the film of Watchmen, and I prefer the film's ending. Makes more sense. In my opinion, of course. This is one that tends to divide people.
OT: Righteous Kill was pretty bad. You could see the "twist" coming within the first 10 minutes. I kept thinking, there has to be something more. There has to be. There's no way they could be that obvious. And yet...they were.
Oh, or how about that awful adaptation of Lost in Space? Can we keep sequel cliff-hangers out of movies destined to never see an actual sequel? Even if you're confident your film is a masterpiece, give it a resolution, people. You can leave one or two MINOR threads open so you have some options, but tie up the main plot and most important subplots so people don't wonder why they've spent 2 hours watching a film that ends in the middle.
And another one that demands recognition is the remake of Planet of the Apes. I'm a fan of the original 5 fans, and I hated this one. The effects were decent, but the story just got stupid. And the ending...gah. It was mindscrewy just for the sake of it, without actually making any sense at all. Annoying. I love twist endings, but have them make sense. Please.