I've long been thinking about how one could approach ranking Star Trek, which has led me back to "what is good Star Trek", and I think it's something like this, in no particular order.
1) Analyzing the human condition.
2) Representing a possible human utopia in a galaxy of troubles.
3) Meaningful performances (not necessarily good acting).
4) Development of stories and arcs.
5) Connection to the episode.
A great episode of Star Trek has all of these things. I'll pick Chain of Command, Part II, as an example. It analyzes the human condition directly - not just with the torture of Captain Picard by Gul Macet, but also by examining how we handle new authority figures thrust upon us. We talk about the human utopia primarily with the Riker-Jellico storyline. They do not mesh, personally, but they put aside their issues to solve a common problem. Basically everyone hits the meaningful performance mark, right down to Marina Sirtis listening to the Captain at the end of the episode. We never really touch on Picard's particular incident again - so I might mark this down for that - but this episode helps establish the Cardassian people as an empire to be feared, one where, should they think they can get away with it, will do abominable things. It really plays up the themes established in the previous season's The Wounded. The episode respects the established Riker arcs, noting his delight in the trombone and his pilot skills. And finally, it's one of the episodes that forms the greatest connection with the audience. Not only do we have the "there are four lights!" meme, we get an unending legacy of moments, we become drawn in to Picard, especially, at a time of great physical challenge, and damn, we get to see the arrogance of David Warner's Gul Macet pierced by Picard's rapier wit. Who among us didn't, for a moment, feel for the pain that the Cardassian villain experienced as a child? And we compare to the utopian human experience of Star Trek - it's something Picard's people would never know.