Very, very close for my top three overall. My favourite is Dr Cox, because he is wit personified. However, right behind him, very closely, is Lucy (from Season 9), because I absolutely love quirky, eccentric, odd people. And Kerry Bishe (who plays her) is amazingly attractive. And then coming up behind her, extremely close call again, is JD, because what would we be without his oddities and inner monologues? And he's basically the male version of Lucy, or rather, she's the female version of him. And I love Zach Braff as an actor anyway, Garden State was bloody brilliant (and had one of my favourites ever film soundtracks too

).
So yeah, close run between Dr Cox at the top, then Lucy, then JD...
Honourable mention goes to Hooch as well. Seems Hooch really is crazy... I never saw an episode of The Suite Life the same way again... ;D