Im going to go somewhat off the beaten track most people are taking here:
Matthew Gideon from the sadly cut-short Babylon 5 spin-off
Crusade.
Here's a captain who isn't just a tired old 'maverick' of the trope that's so commonplace it's downright conformist; from what we do get to see he's genuinely a rogue element. He doesn't take for granted that people are out to screw him over; he's quite happy to screw other people over; he'll use any tool or edge to get his way; he doesn't spend long hours moralising or proclaiming how all he does is for some "greater good" that makes him morally superior, he just gets on with the job; he takes stupid risks not because he's some sort of super-lucky superhuman, but because it's fun or he's already planned out the angles. When he catches someone cheating, he doesn't give a sermon on ethics or ideological purity, he plain asks them to teach him how to cheat too! And yet he still hits a lot of the heroic notes you expect in a leading man. I would love to see a character like his developed.
Best ship...? The Magog Worldship from Andromeda. Its a world. In ship form. Full of Magog. People shouldn't be afraid to go big.
Scarim Coral said:
Why it have to be Captain Buck O Hare of course! He is a green space rabbit and kick ass!
I also endorse this message XD
Honourable mention to Captain Sisko from Star Trek: DS9, for being the only 'real' feeling officer in the whole Trek universe. Let's face it, Captain Picard may be a nice guy to run meet-and-greets with alien species, but when they come knocking with the big guns, I want a do-what-it-takes badass standing over me.