TOS: The Cloud Minders. One of the show's extremely heavy-handed message episodes, this time about classism and labor rights. It's quite dramatically compelling in addition to expressing its ideas eloquently.
TAS: Beyond the Farthest Star. One of the more "normal" episodes of that series, but it really works for me.
TNG: Contagion. One of the most tense and action-packed TNG episodes, featuring computer malfunctions both amusing and terrifying, but also a great showcase for all the characters, and their ability to combine their talents to solve what seems like an impossible problem, to the point that it's one of the episodes that got me into Trek in general (alongside Remember Me).
DS9: Visionary. Pretty good episode of time travel weirdness, and one of my go to examples of what I think is best way to go about explaining time travel: don't explain it, just do whatever wacky shit you want and laugh off the paradoxes with a recurring joke. "I hate temporal mechanics!"
VOY: Latent Image. In addition to being yet another fascinating exploration of the rights and sentience of artificial life, with a hint of an ethical dilemma in there, I really relate to how the Doctor's trauma responses are described.
DIS: There Is A Tide. I love all of the scenes between Admiral Vance and Osyraa.
PIC: The Impossible Box. I remember that being one of the more tense and well-made episodes of the show, especially Soji's existential crisis and Picard's Borg flashbacks, although I find it hard to think in individual episodes with this one.
LD: Veritas. The show hadn't really clicked with me before this episode. I loved the whole theme about the lack of attention the command crew gives to the ensigns, and how this just adds to their problems.
I've only really seen the consensus classics of ENT, and while I have seen SNW and PRO, my favorites are all consensus favorites that get a decent amount of buzz already.
Like I said I've only seen the consensus classics there, and it's been a while. I'm planning to see the rest of it as the Greatest Generation podcast covers it. But it is also probably my least favorite Star Trek show.