Best: Crocodile is the One Piece villain. The bloke oozes pure classic villain aura and was the first big threat to the protagonist in the story.
Other great villains would be Enel, Lucci, Arlong, Blackbeard, Doflamingo, Akainu.
Worst: Vender Decken. I'm pretty sure the only reason people aren't naming him more is either because they don't remember him or they don't want to remember him.
Either way, this stalker pedo villain just adds nothing to his arc, eats up screen time with his gross presence and even has a hideous design just to merely look at.
Decken is the one major arc antagonist that I just genuinely cannot think of a single redeeming feature about. He is absolute trash.