My all time favorite is definitely without a shadow of a doubt, The Joker. He is the anthesis of Batman. The funny thing is the parallel differences between them. Typically the hero is bright, flashy and flamboyant and the villain is dark, brooding and menacing looking. Clearly, that is not the case here and I think that alone makes them a unique pairing. Take the psycosis of it all and mix it in, you have the perfect blend of entertainment and awe.
Now, on to recent... IE, the last 15 years. Bane was definitely there until The Court Of Owls just came and took over that spot for me personally. Talon is a friggin' beast and Batman has got to use literally everything at his disposal to beat them. It's been a masterpiece so far within the storytelling from Scott Snyder.
I do have a soft spot in my heart for Ra's Al Ghul though. If it weren't for him technically Bane wouldn't be. Plus, Talia and Batman spawned Damien... and he's quite awesome. I think I need to re-read "Batman & Son" now...
I also just realized that Jason Todd as the Red Hood was an epic moment in Batman lore as well. I loved it when Jason came back into the world of Batman, I don't however like his current schtick. He was better as a villain IMO... although being in Batman's fold not as Robin is quite an interesting take. I just think he's suited better as a bad guy... and I do want to know the terrible secret he's still hiding.
I also just realized that I've been rambling for quite sometime and I should probably stop. And I never even touched on William Hurt and The Black Glove.