No theories of the female character being Batgirl?!....only kidding....
I think that Penguin is already out of the question. I don't think Nolan has said anything recently, but in the past he's said that the Penguin won't fit in this universe. I'm thinking it will be a more obscure character that he can take a lot of licence with. Perhaps Hush or Strange. Maybe it will be a serial killer type like Zsasz. I would also be happy to see Harley in this movie.
If Tom Hardy is to be one of the villains, I think he could do a decent job with a lot of villains, especially if they are reinterpreted by Nolan.
Since Tom Hardy has been cast, I wonder if Joseph Gordon Leavitt is out of the question. I know you guys may beat me up for saying this, but I think he could do a decent job as a replacement for Heath Ledger (If you don't like Leavitt, go watch Brick right now). Nolan has said that he won't replace Ledger, but I think that Leavitt would be a great addition in another role as well.
I think that the new Batman game, Arkham City, would be a great idea for a movie.
Basically, Arkham Asylum couldn't contain all the crazies, so they put a wall around a big chunk of the slums and called it Arkham City. There's no guards, and they are expected to fend for themselves. Catwoman gets sent there, and the inmates decide to stage an execution in order to lure Batman in.