Even if I think he's overrated in his modern incarnation, Joker blew me away, I'd pay big bucks to see this version again, and in the comics, rather than that one-note Idi Amin level killing machine they have.
Owlman comes at second place because he was such an awesomely evil villain. Love his pun filled monologue to the heroes, as well as the equality between him and Bats.
Gentleman Ghost is awesome. His theme tune is so pimpin', and Greg Ellis does a fantastic vocal performance, can't wait to see him in Trial of the Demon. Along with Black Manta and Gorilla Grodd they seem to be hyping him as a recurring villain, and I have no complaints.
Sinestro was great. I love how unlike other villains his intentions were noble, but he tok things too fa.r I loved the play between him and Bats, and how he didn't feel he fitted in with the rest of the Core.
Black Manta is just badass, hope to see another ep with him.
And anyone tihnk Silver Cyclone tunred out to be one of the best villains. I loved how they fleshed out the Injustice Syndicate's personalities, but he was awesome. His villainous (or extra villainous) reveal at the end was great, and was so proper. If Red Tornado wished to find more about humanity and be more human, then Cyclone would disdain humanity.