John Hamm for Batman. I literally can't think of anyone more perfect (in my opinion). His acting is outstanding, and he looks the part.
Willem Dafoe as The Joker! He's about as perfect for him as John Hamm is for Batman (once again, in my opinion). Everytime I read a comic with Joker in it, it's either Hamill's voice I hear, or Dafoe's.
William Hurt for Commissioner Gordon. This one was especially hard, because Nolan got the casting just so right with Gary Oldman.
One of the greatest British actors for one great character: Geoffrey Rush for Alfred.
When I think Mad Hatter, only Martin Short comes to mind, thanks to his performance during his appearence on that Law And Order SVU episode.
I've always enjoyed seeing Paul in a movie, but I've always liked it more when he had brief cameos in a critical part. (Hangover 2, Saving Private Ryan), and in my mind, he and Loeb just fit.
Campbell for Bullock really fits well. Mostly because I wanna hear that icnoic voice say "commish".
And that's all I can think of. Add more casting choices in the comments, if you want!