Deep Space Nine.
-Incredible individual episodes? Let's see, In the Pale Moonlight, The Visitor, Duet. Check.
-Fantastic cast? Arguably the best from top to bottom of the franchise, including easily the deepest well of non-cast recuring characters (Garek, Rom, Nog, Gul Dukat, Kai Winn, Martok, and Weyoun just to name a few).
-Worthy captain? He might not be as iconic as Kirk and Picard, but Sisko carved his own place in Star Trek history as a more complex character and the man who the Federation needed. The hints of what he'd become can be seen as early as the pilot episode when he uses Nog's freedom as a bargaining chip to keep Quark on the station.
-World building. OMG, yes. We have a world rebuilding after a brutal occupation that has located their gods. We have the dying totalitarian regime trying push off its collapse and justifying its existence. We have an ascendant totalitarian regime. We have, arguably, the most movement in defining the Klingons (impressive as TNG did a pretty solid job itself with them). And we have the Federation, fat and happy through TNG, having to face a civilization-altering threat. Yeah, the Borg were also a threat, but that happened over a weekend. The Dominion shook the Federation out of their Roddenberry complacency and forced them to really grow up in a dangerous galaxy.
-Character development. The most successful Trek at letting their characters grow as the series went along. It wasn't just setting things up to give each character a role, they all followed it to its conclusion. Again, this is true even of the supporting characters. I mean, is there anyone on Voyager with the depth and complexity of Garek or Dukat? Did anyone on TNG grow as much as Nog?
-Overall story. Easily the most successful long-term storytelling that the series has ever attempted. This show built and built so that the series got better each year for its first six seasons. Loyalties change, enemies become friends, and then enemies again. The Dominion storyline was a slow boil, introduced to the series by the machinations of Grand Negus Zek of all characters in a 2nd season episode mostly about a female Ferangi not being allowed to do business (a plot line that, itself, would continue all the way through the show's final episode, though truthfully, not its strongest thread) and wouldn't fully begin until the end of the 5th season. And there was so much going on that it never felt like the cold war buildup was taking too long.
Yeah, there have been other great Trek series. TOS and TNG had amazing individual episodes and a few great characters. But, DS9 put it all together and built what I would rank as one of the top television shows of the 90s. Sadly, Voyager starting so soon after TNG left the airwaves meant that it was treated as a bit of an also-ran.