My thoughts on who they could be;
I also believe Talia Al Ghul could pop up very likely, one reason being there would be another female role. It could be her or Catwoman. And the fact that it would link back to the first movie with Ra's. Most trilogies go back to explore the original movie in some aspect in order to "tie in" the series.
I can see Bane being done, in a truer-to-the-comic way and not a "Batman & Robin" way. Not sure if it would make for a proper closing of the trilogy though, just depends. I would like to see a good Bane on screen, and I agree about Rourke. If done right, and with Nolan that's likely, it would be a great character to have to rival Batman.
Riddler...eh. I don't think it's likely. People say it could be seen as a knockoff of Joker, UNLESS that's what Nolan would go for, someone inspired by Joker. Could be a possible take on the character, but I wouldn't want to see him onscreen. I've always thought of him as boring.
There's alot of BS about the Penguin, even though I thought Nolan said a long time ago he wouldn't ever do Penguin. Obviously if he did write him, it would be the business mogul from the comics but I don't see that happening either. I guess if Nolan even comes back, it's possible.
I think Catwoman is highly likely. I think she would serve perfect as the female love interest/intrique that Batman would question after the death of the last girl he loved. I would love to see Nolan do this character, and with a brunette cast for her.
I'd like to see Two-face, but apparently it's been confirmed he wasn't meant to return. People say he served his purpose anyway and there's not much more you could do, but I don't believe that. He could try to take out the mob/criminals himself, while messing with Batman and Gordon, toying with them. Truth is there is alot of purpose he could serve, you just have to think about it. I really wanted to see him again, if even for a "Scarecrow" type cameo in Arkham or something. I believe Nolan left the ending of TDK open to interpretation for a reason, so I don't believe the character's dead until they confirm it in the next movie. He's such a big popular villian, it's hard to believe we got all we're going to get of him.
Of course there's also the little-known villians, but I think Nolan would stick with the quasi-popular villians in the final installment. I don't see him making up any original villians either.