I voted for Lex Luthor, since he has been the most complex and interesting character on the show and Michael Rosenbaum delivers the best performance of any of the actors (give him an Emmy already !). Lex's story arc/character seems to have truly progressed throughout the seasons, changing as he learns more about himself, his father and Clark Kent. True, he has wavered between being obsessed with Clark's secrets and wanting to be his best friend (who also stays out of his personal business), but he's also slowly developed an intense crush on Lana Lang (btw, I especially admire the writer's craft on that point). One could view Lex's psychological disorder as simply Emmy-bait (it's a bit over the top at times), but it's made him who he is and who he will be. Plus, Lex Luthor is the best role Mr. Rosenbaum has had so far. He deserves it, and he earns it.
Lex and of course Clark are my favorite characters from Smallville. I like Lex because he is teetering on the line of being evil and still trying to be good. He also has a bad boyness to him that I find attractive. Clark is an all around good guy that I like.