TOS: Yeah Kirk is my favorite, though Spock is often very close. Admittedly, some of this the typical guy thing of "this guy gets all the women, carries himself with poise, is smart AND has a swagger about him?! Can I have what he's drinking?"
TNG: Had to be Picard...followed by - would ya believe it - Bev Crusher. Always like eps. where she gets the lead, or gets to take on a challenge, or solve a mystery, like "Remember Me."
DS9: It's ironic, that despite the shows' conscious attempt to do things different than its predecessors, I still wound up liking the shows' big three - Odo, Kira and Sisko - the most. And Sisko is my favorite of the bunch, and my favorite character in all of trek (as an aside, I never really got all the Garak-worship. He's more like a gimmick to more; the DS9 equivalent of Newman on Seinfeld. He's not even in my top five of recurring characters. He did have some interesting moments and lines though).
Voyager: Cross between B'elanna and the doctor, followed by seven, tuvok - and THEN Janeway. Though I like Mulgrew.
ENT: T'Pol. Jolene Blalock is underrated, imo. Reed would be second. Archer did very little for me.