I think it has to be Mr. Freeze. I like the fact that he isn't 'hardcore grungy' like so many other of the villains in the game. He has a sort of soft, calm quality about him. Also, I loved the boss fight with him the most.

How about you?

Mr. Freeze was definitely my favourite boss fight but Joker has to win best villain.

@Dany: Mr. Freeze without a doubt, from the moment he put the suit on and his voice changed to that cold, steel-twanged chill it sent shivers down my spine. He reminded me of The Animated Series, which I've placed on the highest pedestal I own.

Freeze had the best voice on the animated series.  Sadly the guy who voiced him is 89 now.  Not that Maurice Lamarche is bad by any means.   
 
I think the Penguin had the best hideout though.   That place was pretty tricked out for being in a quarantined hell hole.   

The Joker, easily.

I'm a pretty big Batman fan, but I've never paid much attention to Penguin before. However, Arkham City made me love him. Despite how long the character has been around, I really feel like Arkham City is the first really definitive portrayal of the character.

Mr. Freeze comes in seconds though.

I initially read the title as "Favorite Vinny". I now demand a thread dedicated to that very subject.

Freeze, mainly because of how awesome the fight was.

However I never completed the game because my save file got corrupted due to a glitch in the game, so maybe there's a better one with Joker at the end.

I'm going the easy route and saying The Joker.

@Soapy86: Yeah, I was almost going to say The Penguin if only because he is usually so lame that him being a cool and convincing villain was a fantastic surprise :)

Ra's al ghul

@Dany: Mr. Freeze without a doubt, from the moment he put the suit on and his voice changed to that cold, steel-twanged chill it sent shivers down my spine. He reminded me of The Animated Series, which I've placed on the highest pedestal I own.

Mine might actually be clayface; he can be any villain. Id like to see him come back if they make a 3rd game...

Joker was the best obviously, but taking him out of the equation probably had to be freeze. I wish there was more two-face in the game though or I may have went with him.

Mad Hatter. Hi-larious!

The fight itself wasn't amazing, but I loved the part with Solomon Grundy. He was so freaking huge!

This sucks man. This is the number one game I still need to play from last year, and I haven't yet! AHHHHH!