Batman Begins, if you really think about it, didn't have much that could compete with the movies of its year. It was going up against Ray, Sideways, Million Dollar Baby (overrated, but Clint Eastwood was going to get his recognition no matter what), Hotel Rwanda, and on and on and on. It was good in all aspects, but not good enough to make it up there with all of those. Outstanding performances, not so much - Bale is great, but he just kind of did his thing, nothing huge there. Michael Caine had a tiny role, Morgan Freeman, same, Katie Holmes was the only bad part of the movie, Gary Oldman had a tiny part, Liam Neeson had a relatively small part, etc.
The only things it could've got nods for would've been director or cinematography, and the cinematography wasn't hugely special, and director was going to go to Clint anyways.
The only other ones really up there in quality are Spider-Man 2 and Unbreakable. Spider-Man 2, I think Alfred Molina wouldn't have been a bad choice for a supporting actor nod, and Tobey was also pretty good, but not 'best actor' good. Raimi for director? Not even close. Unbreakable should've gotten some serious nods, but it didn't, unfortunately - but then again, I don't think Sixth Sense did, either. Still, that's essentially a different genre.
Someone's probably going to bring up V for Vendetta. No. No way. Not in any aspect.
If Watchmen turns out to have great performances, great direction, great artistic design/cinematography/costumes, etc., I think we'll definition see some accolades fly its way. They're ready to appreciate fantasy and sci-fi, as shown by Return of the King. They just need good material.