So far, I like TOS the most; it's the most fun, the chemistry between the characters is excellent, and it tries to think big even if it doesn't entirely succeed.

After watching almost four seasons of TNG, I've come to appreciate it a fair bit more than I did when I first started watching it (Data is awesome!); it does take itself too seriously, though, most of the aliens are lame, and I don't like Roddenberry's "perfect" vision of the Federation, so I can't rate it as highly as TOS.

I've only seen a few episodes of DS9 and that was some years back, so I can't really comment on it, except to say that I remember it was more in the spirit of TOS and that the weapons looked like cheap plastic toys.

I have no interest in VOY, ENT, or Abrams' Trek, so I'm not going to watch them, therefore I can't comment on them (take from that what you will).

As for my favourite commander - that's Spock (he's my favourite character in the franchise, though, so that can't come as any surprise).