Here's my thoughts on how some of my favorite Batman villains might be able to fit into the universe that Christopher Nolan has created:
Most people who have tried to 'Nolan-ize' Penguin have made him a simple mob boss with a fascination with/fetish for umbrellas and birds, but my take on the character is to make him a toned-down version, stylistically, of the Freak!Penguin introduced by Tim Burton in Batman Returns and played by Danny DeVito. What I mean by this is that you retain the disfigured/deformed nature of the Penguin's physical features, but do away with anything that takes him into over-the-top, circus-freak territory (such as the eating of raw fish and living in the sewers with genetically engineered penguins), and make his motivations revolve around his own personal psyche issues and the way that he perceives the world in relation to his deformities/disfigurations (similar, in some ways, to the way that Nolan and Heath Ledger characterized the Joker). Nolan won't ever use the character, unfortunately, but, if the WB decides to keep the more realistic tone established by Nolan in future, post-Nolan films, I could see a future director or directors deciding to use the character.
My favorite version of Clayface (the Batman: TAS version) is, unfortunately, an impossibility in terms of fitting Nolan's Bat-verse, but I don't think it's impossible for any
version of the character to exist in Nolan's universe. It wouldn't be that difficult to make Clayface an assassin or spy who uses an experimental cosmetic compound (in a world where you have the existence of stuff like memory cloth and sonar waves, stuff like a 'living mask' wouldn't be entirely out of the question) to change his appearance at will. You could even make him a member of the League of Shadows if you wished.
I liked the way that the short-lived Birds of Prey TV series characterized Harley Quinn, although, for the purpsoes of the Nolan-verse, I think the best approach to utilizing the character would be, as in the case of Batman: The Animated Series, to make her a female version of the Joker, particularly the Joker as played to brilliant perfection by Heath Ledger. I don't think Nolan himself will use the character, but if the WB does decide to keep the more realistic tone of Nolan's films in future, post-Nolan films, she is definitely a character that I could see being brought in.
Andrea Beaumont is a villain that is, quite frankly, tailor-made to fit into Nolan's Bat-verse, and is a character that I've mentioned I would love to see him include in TDKR, since she fits both of the two criteria that have been set out in terms of the roles that Nolan is casting for (a love interest and a villain). She also makes sense in terms of the 'status of things' in terms of the political and social climate in Nolan's version of Gotham as established by The Dark Knight, and is a villain that could be lifted, wholesale, from the source material (Batman: The Animated Series) in which she appears.
Most people seem to think of a Nolan-ized version of Catwoman as being a villain, but, for me, the perfect utilization of the character in terms of Nolan's universe would be to use her as a 'stand-in-' for Batman, especially after the events of The Dark Knight. Characterization-wise, I think she works best if you draw on those elements of her character which classify/identify her as the female equivalent to Bruce/Batman, and make them the 'core' of who she is and the role she plays.
Christopher Nolan might feel otherwise, but I don't think Mr. Freeze isn't as impossible to adapt into his (Nolan's) more realistic universe as one might assume; cryonic technology does actually exist, and, in order to make it fit Nolan's universe, all you would have to do would be to make a 'realistic extraploation' in terms of the technology as it exists now and where/how it might exist in the future. Chracterization-wise, the character would need to be lifted as much as possible from Batman: The Animated Series, although you might want to tone down his obsession a bit so as to make him and his motivations more believable and less over-the-top.
Most people that I've seen try to 'Nolan-ize' The Riddler have made him a serial killer or something, but, personally, I think that you could very easily and feasibly adapt either the Frank Gorshin or Jim Carrey versions of the character into the Nolan-verse, although you would definitely have to tone down some of the flamboyant, over-the-top aspects of how both Gorshin and Carrey used their acting talent to bring the character(s) to life. Speaking of Carrey, one of my 'pipe-dreams' is in fact to see him 'reprise' a less overtly flashy and over-the-top crazy version of the Riddler character in Nolan's universe, and, although it isn't going to happen with Nolan in charge of the franchise, it's something that I think you definitely might be able to pull off in future films should WB decide to retain the realistic tone of the universe that Nolan established, provided Carrey himself was open to the idea.