I don't really consider Catwoman a villain in the Nolan trilogy. But I did like her portrayal as an anti-hero. And if this is asking my preferred character rather than favorite villain, I'd probably put her up top.
I like Ra's al Ghul. I find it interesting that he's pretty much how Batman would be if he went too far, seeing how they have the same training. Bane's really cool, too, but his voice was hard to understand at times. Talia was also great because of how she was the puppet master who pulled all the strings in Bane's plan, but they picked a terrible actress to play as her. That was the worst death scene ever...