I have to say TOS Best: Wrath of Khan.
Yeah I know, it was a movie. But it's so much a "Part 2" you almost HAVE to include it.
Besides, to paraphrase Comic Book Guy: BEST...TREK...EVER.
As awkward and disappointing as some of the Season 1 and 2 episodes of TNG could be, you HAVE to give props because they retired the Starfleet Mini for female characters about the time S3 kicked off. Those girls just looked SO good.

Which ties into:
Best DS9: Trials and Tribble-ations.
The look on the Time Travel Investigators' faces when Sisko said they encounted the original
Enterprise ("Oh HIM...." ROFL! ) was priceless. It was a good all around episode, and I LOVED how well they integrated the original footage with the new (how many 24th Century Starfleet officers can say they brawled with Klingons alongside Scotty and got a dressing-down by Kirk HIMSELF?) Odo smitten with the tribble (mirroring Spock's own "illogical" affection from the original episode) and Quark's irritated expression when they've taken over the Promenade at the end. The entire crew poking fun at Worf's recounting of his peoples' "glorious" battle to exterminate them. Bashir possibly being his own grandfather. Sisko risking the timeline to speak at least ONCE with Kirk ("I'd have done the same." Lol!)
And of course, Jadzia in the Starfleet Mini. Rowr! ("...and women wore less!")
