I decided to divide this into 'top-tier' villains and 'secondary villains'.
Top-tier villains
The Penguin: I've long felt that the most interesting version of The Penguin was the 'Burton Penguin', and would like nothing better than to see a variation on that version of the character incorporated into the 'Nolan-verse'; it would make the character so much more interesting than just your average 'mobster', yet give Nolan and Co. a way to seemlessly integrate him into the existing mythos of their Bat-verse with very little trouble. My ideal 'Nolan-ized' Penguin is a partially physically deformed man whose fortunes rival that of Bruce Wayne's, but who has built said fortunes illicitly. His involvement in the story would see him try and assume part of the mantle left behind by Harvey Dent, while at the same time undermining Gotham society from within the criminal underworld. This would not only allow him to fill the even larger void in Gotham's mob community left after the events of The Dark Knight, but give Nolan and Co. a way to facilitate Batman's re-emergence as the hero Gotham both needs and deserves.
Catwoman: Out of all of Batman's 'top-tier villains', Catwoman needs very little modification from her traditional comic book roots to fit into the 'Nolan-verse'. However, the way I think she can best be utilized is as a secondary villain akin to the Scarecrow in 'Begins' (IOW, as a way to demonstrate how Batman's fugitive status - and the aftermath of the Joker's rampage - has left Gotham's underbelly open to colorful and inventive 'master criminals').
The Riddler: The Riddler is another one of those Batman villains whose origins and mythos would need very little modification to fit into the 'Nolan-verse'. Unlike other people who've tried to modify the character, though, my ideal 'Nolan-ized' Riddler is an amalgamation of the 'Frank Gorshiin' Riddler from the 60s TV series, the 'Jim Carrey Riddler' from Batman Forever, and the DCAU Riddler; a brilliant, if slightly 'off-kilter' man whose eccentricities - coupled with tragedy - have led him to become a master criminal. I think his ideal role is, like Catwoman, to demonstrate the full effects of what The Joker was able to accomplish in The Dark Knight, although he could also work as a more 'primary' villain (ala the Joker and my 'Nolan-ized' Penguin).
Secondary Villains
Clayface:
'Batman Begins' proved that it's not impossible for some of Batman's more 'out-there' antagonists to be treated in a realistic fashion, and, given the technology levels of today's society, it would take very little for a 'Nolan-ized' version of the Clayface character to work. As with The Penguin and the DCAU version of the character, a 'Nolan-ized' Clayface would need to be someone with physical deformities - either 'natural' or caused by circumstance - and his 'powers' would need to be a result of whatever it was he was using to cure his deformities or physical imperfections. For the sake of believability, you could also tie in the nature of his 'powers' to the Fear Gas epidemic from 'Begins'. In terms of finding a role for the character, I think he's best left to being an 'escalation example' villain (ala Catwoman).
Scarface: Given the direction that Nolan and Co. have gone with their Bat-verse, I'm rather surprised that we haven't heard anything about the possibility of the character of Scarface showing up as part of the new film franchise, since he's almost tailor-made for the universe that Nolan and Co. have envisioned, especially in light of what happens in The Dark Knight. As with The Riddler, Scarface could work as either an 'escalation example' villain or a primary villain, depending on the storyline. He's also one of those villains - ala The Joker - whose exact origins wouldn't even need to be explained.
Harley Quinn: If there's one secondary Batman villain who could really come into their own in the 'Nolan-verse', it's Harley. The WB's 'Birds of Prey' TV series had its share of problems, but one of the best things about it, IMO, was its utilization of Harley Quinn, and its explanation of why she was doing what she was doing. A 'Nolan-ized' Harley would need to either be a doctor that The Joker met in Arkham, or else someone who came to Gotham in the aftermath of his (the Joker's) rampage and became obsessed with uncovering his motivations and delving into his psyche, leaving her open to manipulation by him. She could then branch off on her own in an attempt to 'finish what he started', making Batman's life even more difficult, or else be part of a plan for him (The Joker) to break out of Arkham and continue his rampage in person.