Salvatore Maroni (If a reboot is started): George Clooney
Rupert Thorne: Joe Pesci
Edward Nigma/The Riddler: Adrian Brody
The Penguin: Philip Seymour Hoffman
Poison Ivy: Jessica Biel or Cate Blanchett
The Joker: For a Nolan-style Joker, Joesph Gordon Levitt. For a comics style Joker, Jim Carrey.
Harley Quinn: I've seen lots of suggestions in the Harley Quinn thread for who should take the role, and they're all annoying blonde actresses
(Kristen Bell? Sarah Michelle Gellar? Uck.)
Just becuase Harley is blonde in the comics doesn't mean the actress playing her has to be. (Any actress can make themselves blonde for the role. It's called makeup people!)
I think Zooey Deschanel would stay true to Harley in the cartoons/comics, but for a new take on the character, i'd say Helena Bonham Carter. Sure, she's a bit older, but she is a great actress and has experience playing odd characters.
Harvey Dent/Two-Face (If a reboot is started): Daniel Craig
Bane: Brad Pitt
Deadshot: Leonardo Dicaprio or Ethan Hawke
Roman Sionis/Black Mask: Gerard Butler