For me it was a hard call between Stardust and Apollo 13. Both excellent movies - and very, very different.
Stardust is very different from the book, which I adore. I don't think the best things from the book really made it in the movie. On the other hand, the best things in the movie weren't in the book. Both are great for the mediums they are in.
Apollo 13 is the world's best SF movie that, uh, isn't SF.