Willem Dafoe would be neat to see as Joker. As we all know, he can do maniacally over-the-top, and I saw more Joker than GG in SM '02. Plus, he practically is the Joker's twin - facial structure is dead-on.
Johnny Depp as the Riddler, his humorous side is somewhat more subtle and I can see Depp fulfilling that.
Patrick Stewart as Mr. Freeze, he resembles the BTAS Freeze and can surely be intelligent yet ruthless (if they ever portray him like that again...)
Now, here are some I'm iffy on, but they could work...
Big maybe here, but Nicolas Cage as Gordon? He has a very Gordonesque look, and isn't as bad as some say he is.
David Tennant as Crane, he is also good at being maniacal but can be serious if need be:
Helena Bonham Carter as Quinn? She IS Bellatrix IMO, did a phenomenal job as her, and Harley wouldn't be much of a stretch.