You didn't specify main characters, so I'm going outside the box:
Favorite: Captain Proton
Worst: Captain Dirgo (TNG: Final Mission)
I don't want to vote yet since I haven't seen all of TOS or ENT.
From what I've watched (VOY, DS9, and TNG)....I have to say I love both Janeway and Sisko, although I think Janeway has more personality. Also like Picard of course.
Sooooo....Can I also vote for Captain Proton? I don't dislike anyone!