For me, with the possible exception of Christian Bale, everyone in the Nolan-verse movies have essentially seared themselves into my mind as the iconic representations of the characters, so I won't even bother listing those characters.
Tim Drake - I can't think of anyone better, so I'm OK with River Phoenix
Dick Grayson - Here's where I expect to hear some guff. Disregarding skin color, I think a young Will Smith would be perfect for Dick.
Jason Todd - Joaquin Phoenix
Barbara Gordon - I keep going back to Dina Meyer. I'm having a hard time thinking of someone better...
Catwoman - Angelina Jolie
Mr. Freeze - Leonard Nimoy
Riddler - Bob Hope
Harley Quinn - Jenny McCarthy as a live-action version of the cartoon, but as someone young, beautiful, and talented who could have played a great Harley opposite Heath? Scarlett Johansson.
Penguin - no one... ever... will come close to Burgess Meredith. Although, I will say those Philip Seymour Hoffman rumors aren't terribly upsetting.