TOS: This might be the hardest to pick - maybe "The Corbomite Maneuver"? It's fairly well-known, but is crowded out in a season full of classics.
TAS: Pretty much everything besides "Yesteryear" is underrated, but if I have to pick one, I'd pick "The Magicks Of Megas-Tu" for sheer weirdness.
TNG: "Remember Me" - really good episode. I think it's pretty well-regarded, but it should be better regarded.
DS9: I've always been very fond of "The Sound of Her Voice," for some reason. I don't think I'd ever seen anything quite like it when it originally aired.
VOY: I think "Counterpoint" is the finest episode they ever did, but people rarely talk about it.
ENT: Uh...I guess I'll say "Daedalus" - it does a lot of worldbuilding surrounding the transporter, but isn't one of the big "lore" episodes that people tend to talk about.
DSC: "Su'Kal". The cause of the Burn is something that speaks to the humanist core of Star Trek in a way that many people seem to overlook.
PIC: "Remembrance." The first episode of the series is nearly perfect.
LD: I don't know if the nature of the show lends itself to this exercise, but I'll say "An Embarrassment of Dooplers".
PRO: "Crossroads" - the kids arriving at a turning point, and making the kinds of dumb decisions that kids make.
SNW: "Ghosts of Illyria," I guess - this series is still pretty fresh, but this is one of the better episodes that isn't a "gimmick" episode.
Remember Me was one of the episodes that got me into Star Trek. My parents loved TNG and Voyager, but it was one of the first episodes I actually sat down and watched with them, and the whole premise of everyone disappearing, and how Beverly figured out what was going on, hit my brain in just the right way.
@ipacialsection@ValueSubtracted I rewatched "Remember Me" recently and it's deeply chilling, even knowing how it's going to end. It's like a classic "Twilight Zone" in all of the right ways.