David Hyde Pierce is someone I never considered but would be great. The top of my list is still Edward Norton and Jude Law, though I can see Anthony Michael Hall doing it.
The Riddler and the Joker are my favorite Batman villains, and when I say those two together I mean the incarnations where one isn't a cheap knock-off of the other. I like the cool, calculating Riddler like the one in the animated series. He's one hell of an interesting villain and he can really have some depth to him besides his silly gimmick if given the chance.
Also, I really find most villains would fit perfectly into Nolan's world. With Scarecrow's fear gas and hallucinations and the mask sans the straw outfit, Ra's Al Ghul's hints of immortality, the Joker's whole spiel as well as Two-Face around the corner, I don't see why others wouldn't fit perfectly into the world Nolan's created. Catwoman is a cinch. The Penguin could be a physically deformed guy they call that because he sort of (and I mean sort of) looks like one-there are guys I know given nicknames because they resemble things like that. The Riddler doesn't have to wear the spandex with the question marks all over it. As a matter of fact, the animated series outfit seems like something Nolan could live with, and so could I. It's not so outlandish that it breaks the tone but it's also VERY Riddler. A question mark tie is good enough for me.