Since this thread is kind of revived, I would have to say Xemnas is my favorite. I love both his English and Japanese voice actor, he seems very smart in the way he talks, he has really cool hair, and he just makes a very good villain. My second favorite would be a tie between Xaldin and Axel.
Huh you don't usually hear Xaldin as being towards the top of someone's favorite Organization member. I will say he is a pretty interesting character what with his stance on love and trying to turn Beast into a Nobody.