Firstshowing has news that there's a studio casting grid (basically a document listing the roles in an upcoming project) with the Riddler listed. If true, this means the Riddler is the villain. According to the source, Joseph Gordon-Levitt is listed as 'interested.' Again, if true, this does not guarantee that he'll do it. Just that he's a leading candidate.
After The Scarecrow, Ra's Al Ghul, The Joker, and Two-Face, who should be Batman's next enemy in the Batman Begins/The Dark Knight series? Well, as of now we know that Tom Hardy will play Bane and Anne Hathaway will play Catwoman.
Check out the master list for all the villains covered. I've pretty much run out by now. Obviously, there are more Batman villains, but not any of significance that I know of. As of February 2009, no one is confirmed as a villain. Not the Johnny Depp Riddler, not Phillip Seymour Hoffman Penguin, nobody.