But the answer is so obvious... Lex Luthor!
No! Lex Luthor is the absolutely most annoying villain they had! How many times can you come back and annoy people? What made him even more annoying is that he came out clean almost every time, until House of Luthor, when Clark&co decided they have to find some dirt about him. And they couldn't do that earlier? Even more annoying were the two wedding arcs, Lois/Lex and Lois/Clone/Clark.
The two best villains were Tempus and the Prankster. Smart and sarcastic, and really cool. I chose the Prankster, but I think I like them equally.
Julie