I think Archer is my favourite character on Enterprise, though perhaps because he's the best of a weak bunch. Kirk is nearly my favourite on TOS, but McCoy just beats him to it. I do love Kirk though.
Beyond that...well, I do like Picard a lot, though I prefer Riker and Data. I like Janeway too (never quite got all the hate for her), but the Doctor is better by a long way, and I prefer Paris as well. As for Sisko, while I don't dislike him, I prefer almost everyone else on DS9.