My favorite Would have to be Cpatain Janeway. She is very wise and ambitious. However, she seems a bit arrogant. My second favorite is Picard. That accent is what makes him a good Captain.
My all time favorite captain is Captain Taurik!
But seriously:
1) Picard
2) Janeway
3) Sisko
4) Archer
5) Kirk
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6784) Jellico
(I hate Jellico)
LOL Who doesn't hate Jellico...seriously! He was way too arrogant on the Enterprise when Picard, Worf and Beverly went on the "Secret Mission"
1) Sisko
2) Picard
3) Janeway
4) Archer
5) Kirk
6) Riker (At the short moments he was captain :P)