Each has his/her own merits. Again I have to say that my favorite is only by fractions of a percentage point. My favorite is Archer because he didn't hesitate to use "Agressive Negotiations" when needed but he didn't need to find a female to bed on every planet either.
The best qualities of Kirk and Picard, roled up into one captain.
Picard is my man, hands down because he embodied everything that Trek has come to mean to me. Kirk was the first of course and the one everyone had to follow but I didn't like his "girl on every planet" mentality. Janeway did well in a very bad situation but did a bit more fighting than thinking. Sisko was just sort of an Administrator to me, not really a Captain and I didn't see enough of Archer to judge him. So, for me it will ALWAYS be Jean-Luc Picard :)
My favorite Captain is Janeway. Shes bright, tough and beautiful. Shes been in jams that would stump Kirk, Spock and McCoy. She and her crew survived seven years out there without contact with Starfleet Command. She and her crew were like an uncontrolled labratory test of Starfleet survival and skills. She also had the only ship in the fleet to have an artificially intelligent medical officer. She dose a great impression of Picard. She has crossed swards with Q several times.
All in all, there should be more female captains in the fleet.