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.
Devil in the Dark is one of the scariest episodes of TV ever.
Ricardo Montalban playing the manipulative tyrant in Space Seed never gets old. Much better than his crazed mad man in Wrath of Khan. "Now you must ask to stay." The rest of the episode is flawed.
The episode where Cisco plays a 20th century sci-fi writer is Emmy-worthy. I haven't seen much DS9, but if it's all that good I'm missing out.
Recently, S02E02 of SNW, a "trial" episode, was surprisingly riveting.
DS9 is probably the strongest of the TNG-DD9-VOY-ENT set, partly because they wrote stories with arcs across seasons and episodes and not just syndication-friendly reset to zeros. It also benefits from most episodes taking place entirely in the station, so they don't need to spend as much time introducing the strange new world or the new forehead aliens.
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.
Whenever I think of my favorite episodes, I think of what are probably the cliché and blatantly obvious ones: In The Pale Moonlight (DS9 S06E19), Measure of a Man (TNG S02E09), and The Inner Light (TNG S05E25). TNG and DS9 are my most rewatched Treks, so they are always freshest in my mind.
You bringing up Living Witness (Voyager S04E23), though, has reminded me of how phenomenal an episode it was—and I completely agree with it being a top five. I have my problems with Voyager, but, from time to time, it could crank out some truly classic Trek.