My preference

1. TOS & TNG - it's hard to decide, I love them both

2. TOS movies - yeah, even 5 has some fine moments

3. Enterprise - I loved the first 3 seasons and was bored by the 4th

4. DS9 - weak start, actually VERY weak, but when they started to concentrate on the Dominion story arc it got really, REALLY good

5. TNG movies - they look pretty, but except First Contact and some parts of Insurrection nothing makes any sense

6. Voyager - I never liked the show, actually this was the first Trek show where I HATED some characters (the Borg kids, Neelix, that Naomi whatshername kid, the holographic doctor, the Borg - OMG they managed to maked the Borg BORING - how is that possible?). I started to like the final episodes spread over the last 2 or 3 seasons, the story arc when they started to show the team in the Alpha quadrant trying to bring them home

7. TAS - some episodes are really great, but most of them are just too childish, the animation is full of errors, the score is repetitive and actually annoying...

8. JJ movies - there are 2 things I like about the new movies - the score and the new McCoy. Everything else sucks imho.

Commanders

1. Kirk & Picard - I love 'em both, each of them for different reasons

2. Archer - if I was in a military organisation, this is the kind of guy I would follow to battle

3. Sisko - I didn't like him originally but I got used to him very quickly

4. Janeway - never liked her, don't know why, maybe because of her "inconsistency" - in some episodes she's the good mother of the crew, in some episodes she's an action hero, in some episodes she's a very "girly" woman, in some episodes she follows strictly the Starfleet principles, in other episodes she's like "to hell with the Prime Directive" ...

5. JJ Kirk - I still think Pine's version of Kirk is simply an asshole, not sure if it's JJ's fault or Pine's