This was genuinely difficult because I really like Sisko as a captain (despite finding DS9 significantly lacking in entertainment value) but I also feel Janeway is just awesome. I've opted for Janeway because while she can't pack a wholloping punch and one could argue she is not as effective as a captain in general as Sisko might be, she was better in my experiences (I haven't seen the complete series of DS9) as a captain under pressure, as a captain who had to make difficult calls and generally just had a great mean streak to her. I also enjoyed her sense of humour.

Very hard choice, though. Oh, what's that? Kirk? Only if you count the recent movie. Shatner just never 'did it' for me.