My personal top five Star Trek episodes from across the franchise. My opinions are not designed to be controversial, but in the past they’ve been molten hot in Trek groups. Numerous well regarded episodes that are the consensus tops don’t make my list, and in fact TNG is entirely absent.
Living Witness (Voyager S04E23). My all time favorite Trek episode. It deals with the serious ideas around twisting history into a narrative for personal and political gain, and in the same episode has so much deadpan comedy with the depiction of the evil Voyager crew.
In The Blink Of An Eye (Voyager S06E12). A great episode that followed the evolution of a society that looked up at the mysterious starship Voyager in orbit. The episode never really had an antagonist, but was more focused on social interactions, and at the end the cooperation between societies.
Balance Of Terror (TOS S01E14). The most engaging depiction of starship combat in the franchise. The running fight resembles submarines playing cat and mouse, with victory relying on wit rather that raw firepower. Also Romulan reveal.
Devil In The Dark (TOS S01E25). The classic tale of not judging a book by it’s cover.
It’s Only A Paper Moon (DS9 S07E10). An exceeding rare example of PTSD in media that doesn’t lean on the crutch of in-you-face flashbacks, but instead shows the slow slide of a realistic depression and withdrawl into a safe corner. Also confirms yet again that the Starfleet psychiatrist division is useless.
A favourite of mine is Civil Defense (DS9 S03E07). A series of escalating attempts for Gul Dukat to assert control over DS9. It leads to some very satisfying Gul Dukat encounters, who in my opinion is a fantastic villain throughout.
I agree that Gul Dukat is fantastic, but calling him a villain implies he ever did anything wrong.