It depends on which version of batman: Adam West series, animated series, movies from the 90s, the new movies. Heath Ledger as the Joker was amazing, but overall my favorite is Two-Face.
Twoface is a simple, yet somewhat brilliant villain! So I HAD my money riding on him... =D
...but...
...THEN I saw "The Dark Knight" and the way the Joker was presented by Heath Ledger was simply E.P.I.C.! So, since the Dark Knight, I changed my like-of to the Joker! =)
That is... untill the next movie comes along and TwoFace returns maybe?
Joker was my favorite, and not just because of Ledger, who was absolutely amazing. I enjoyed the insanity that he had and the way that he seemed to have no plans whatsoever.
Out of the campy 60s Adam West Batman tv series I think my favorite villain was False Face.
Moving into the 80 to early 90s movie series I will have to go with Catwoman, though Jack Nicholson role as the Joker is a close second. All the other characters I thought were ridiculous in one way or another.
The 90s Batman The Animated Series, this is a pretty hard choice to make here given so many of the villains were so well developed in that series. The Joker, Two Face, The ventriloquist with Scarface, Baby Doll, I could keep going. I guess if I were to go with the best from the perspective of development I would have to pick Two Face, since we actually get to see him having a normal life as Harvey Dent in episodes before the one involving the accident that turns him into Two Face. So we actually got some build up of his character spanning more than half an episode before he goes rouge.
2000s The Batman, I didn't really get that into this series since to me it felt like a sort of watered down version of the 90s Batman The Animated Series. Really the only villains that stick out in my head are Catwoman, The Joker, and Scarface/The Ventriloquist. Catwoman sticks out only for those ridiculous looking goggles they gave her. I think they played up on The Jokers psychotic funny personality in this one to the point of it being overt. So My pick here would be Scarface/The Ventriloquist I think they did a pretty good job with his battle between the two personalities.
Batman The Brave And The Bold., I actually didn't like this series much at all at first but it kind of grew on me as I watched reruns. As for favorite villain I would have to make it a toss up between Owlman and The Joker. They seemed to me like the only ones to handle the intentional campyness with the most respect and Joker he sort of fit right in. I guess with a pick between the two I would go with Owlman only because Joker was a bit to easy to write for in this setting.
Finally the latest Batman Dark Knight movies, As cliche as it might be Heath Ledger's Joker. I liked how he combined elements of the past Jokers and created this complete anarchist character.
I have only watched The Dark Knight, but I find The Joker a very cool villain. The way he plays with this victims when he tells them a random story while holding two blades in their mouths.
There are so many different versions of Batman, you'd have to specify. I actually mean any batman villian! you can pick from whichever movie or book so long as its an actual batman villian.