After Batman Begins, I remember Nolan and Goyer mentioning a basic outline of the second and third movies. It was basically this:
Movie 2, Joker is the villian, Harvey Dent helps bring him down.
Movie 3, Joker scars Dent at the beginning of the movie while at trial for his crimes, Two-Face is the villian.
The thing is, they combined it all in the second movie to make Dent the big character. I've read in interviews that Nolan wants to wrap everything up in this movie. In a way that you can't really do in comics, because the story never stops going.
I don't think Bane, Killer Croc, or Poison Ivy are going to be in it, just because Nolan wants to go as realistic as possible.
Honestly, they'll probably go with whatever villain fits the kind of story they're trying to tell, as opposed to picking a villain and writing a story around them.
I could see Catwoman being in there somewhere. Mostly because there's got to be some female lead involved.