TOS: The Kirk/Spock/McCoy dynamic is quite possibly the best such friendship in Trek, Starfleet is as honest about its military background as it will ever get, and the Enterprise actually feels like a real ship. Also best episodic music.
TNG: Accessable to non-fans while at the same time offering something for regular viewers, excellent insight to alien cultures, some of the more memorable characters in Trek.
DS9: Best utlization of all the main cast, plus prominent parts for recurring guest stars and a long-term story arc that actually got resolved.
VGR: Best action scenes, good story ideas, excellent ship designs. Best theme music.
ENT: Best visuals.