Late TNG / Voyager era for me. It's just about the time that things get that "just right" feeling. There isnt a lot of war, exploration is still prime objective and the technology is before time-travel ships start mucking it all up. Honestly the utopian atmosphere / ideals and technology is what I like the most about Star Trek. It gives me hope that maybe someday we can finally achieve something worth while. Money and greed are not the guiding force in the universe and you can persue what interests you instead of just getting a paycheck. Once replicators actually come into existence, than material wealth really isnt an issue, you want something, you just replicate it. And people will make new things all the time, not because they are paid to make a product, but instead because it's a true labor of love. People will do things for the right reasons, rather than "can I crush my competitor". So, yeah, TNG all the way.
TOS was too cowboy, Enterprise had too much turmoil (Terrans were still too much like we are now, with greed, racism and fear of the unknown, screwing things up).
Nothing like peace and the pure pursuit of knowledge to enrich the soul properly.
TOS (I'd love to pilot an Excelsior Class with the bridge from ST:VI). Plus, I like the TOS Klingons best; I think they work best as an enemy species, but before the whole "honor" thing got out of hand.
To be quite honest, I'd really rather not be a captain. Too much responsibility; I'd much rather let someone else tell me what to do. So I'll just say that if I was in Starfleet, it would be TOS era. No hardcore war going on, 60's hairstyles, and I could wear a skirt. Only way it could get better was if Starfleet issue boots were high heeled.
If I could be a civilian on the other hand, send me off to DS9 era so I could run off with Gul Dukat.
TOS hands down. There was more of an exploration feel to being a starship captain at this time. They were out there basically on their own upholdong their values and what they stood for because of lack of communication over long distances. The only way'd ya get me to captain a ship in the TNG era woud be if it was in Voyager's position. ENT era... No exactally my cup of tea. Couldn't stand the Vulcans watching over my shoulder.