I love Buggy as a character but I don't really portray him as a villain anymore. Arlong was cool and I really liked the fact that he was an evil bastard towards human but genuinely cared about his crew. I'm sick of those villains who kill their companions without a valid reason. Just because it makes them look more evil.
Croc is also one of my favorites… Most of the reasons have already been said.
But I think my favorite villain is still Rob Lucci/CP9.
Unlike some people, I don't compare Lucci to other animanga villains. I only compare him to OP villains and when I look at him like that, I really see how different he's from all the other major OP villains. He doesn't have that sterotypic distant laugh and he kept his dignity to the end unlike the others. I also really respect the fact that he doesn't totally rely on his DF powers. He really is a combat master without always having to use DF tricks, thanks to hard training and Rokushiki. Crocodile and Enel would be nothing without their powers. They are strong yes, but the fact is that they almost always rely on their logia-powers unlike Lucci who usually transforms only when he really needs to.
And Lucci's DF power is also one thing I like. I don't give a damn how many people say zoan powers are "gay". I like Lucci's power espesially because it's something different. I have noticed this pattern that all major villains always tend to have a logia-fruit. Logias are cool but I really wanted something different and Lucci offered it.
Because of these traits, I really started to like him. Then there's of course these other reasons like his elegance and looks, Hattori (love that pigeon...very original idea) and his overall way of acting. I like it that he's very silent guy who isn't boasting all the time or just being an ass towards his co-workers.
I also really really like the other guys of CP9 and this villain group in overall. They are cool and mysterious and they also offer enough variability: There are calm, collected guys but also weirdos and a very clumsy chief. Only Califa was pretty dull to me because her only purpose seemed to be fanservice.
The arcs with CP9 were very emotional and convincing, they managed to create this real sense of threat. CP9 had... and still has a great effect on me.