After many discussions with friends who have seen DK, and reading the posts on here, my personal belief is that Bane would be the logical choice for a (potential) third movie. Given, I dont know the Batman comics as well as some, so there may be people I am missing, but, as mentioned before, the logical choices could be (with my own reasoning):
Harley - easily enough to explain where she came from.... possible to make a 2+ hour movie with just her as the sole (primary) villain? I doubt it. Easily explainable back story though... maybe a support villain role?
Riddler - It's possible to give him a legit/realistic back story... and while many people who enjoy the character might enjoy seeing him done well on the big screen, I don't think the masses would differentiate the Riddler from the Joker. I mean, Riddler, from what I know, isn't nearly as sadistic as Joker is, but really, I think everyone who sees Riddler is going to automatically compare him to the Joker. I would be shocked if the Nolans chose him for the third installment.
Bane - Given the finale of DK, I think Bane could be easily reworked to be a Bounty Hunter / Hitman / Mercenary, who is trying to catch / kill / break the batman for a reward / payday / fun, because the public / mob / inmates don't want the Batman around anymore.
I think, given Nolans direction with the new Batmans, to me, Bane seems like the logical choice (removing the whole Venom drug thing). And personally I like the mask (maybe not a gimp mask) but I'm sure they could make it look cool, and probably give a good explanation for why he wears it.
My 2cents.
Also... Pencil Trick = awesome. But I think the best scene with the Joker is still the one with him driving the cop car (As seen in the trailer) with his head out the window... There was just something in that shot... I dunno what....