For Batman:

Gambit. He's a thief and he has that Joker/Riddler vibe to him.

For Wonder Woman:

Rogue. Storm was my initial choice but she's not really a villain-type.

For Superman:

Professor Xavier. Supes may or may not be psi-proof, but that doesn't mean that Charles can't manipulate other people into fighting the Man of Steel. They're exact opposites.

Quicksilver for flash...Wait no.

Colossus for Martian Manhunter.

Magik vs Zatanna

Cable vs Flash

archangel or Longshot vs nightwing

Wolverine vs Alfred...

Domino vs Huntress

Magma vs Martian Manhunter

Magik vs Superman (is superman still vulnerable to magic? I haven't read DC in almost a decade)

Gambit would make an interesting villain for Nightwing.

Namor for Aquaman :D

Angel for Nightwing.