I would put Batman Begins in my upper tier of superhero films, but not right at the top. The problem with the film, versus a film like Spider-Man 2, is that the villain story and the supporting characters are just there. They really don't hold their weight next to the main story, which is Bruce's origin. And as Kevin mentioned earlier, I didn't quite feel the Batman mystique whenever Bale put on the costume. And lest I forget the really shoddy attempts at action sequences.
Whereas with Spider-Man 2 (which I feel is the most complete superhero flick to date) everything in the film matters: Harry's story, Mary Jane's story, Octavius' story, May's story. And it's all tied together. Not to mention the action sequences were kinetic and imaginative. The thing I will say, though, is that Begins was far better paced than SM2.
But in the end, I think a lot of fans mistake Begins' "darkness" and "edginess" for quality, and chide Spider-Man 2 for its more light-hearted moments and dub them "campy". I just don't believe in that mentality, whatsoever.