Tos.
"Trouble with Tribbles" because the tribbles were so durn cute

LOVED "Mirror, Mirror" mostly because the darker universe was so different from shows of the time.
"Balance of Terror" the intro of the Romulans was a great way to add a more complex villain to the mix as well as subtle concern about Vulcan loyalties.
TNG.
"Time Squared" I think that's the name of the ep when the Enterprise loops in time and Data has to send himself a message in the form of clues. I'm a sucker for stories that have a well developed time theme.
"Perfect Mate" my absolute favorite! I loved how bittersweet and emotional it was on so many levels.
"The Measure of a Man" I'll admit it. The thing I liked most about the ep was that Data's recording of Tasha was found.
DS9.
"You're Cordially Invited" because there is so much to love about this ep. Martok, Martok's wife, Dax's meltdown, Bashir and O'Brien chanting "Kill Worf" the first view of a future bathroom (wow, people actually still have them in the future?) that I could ever remember, a bachelorette party. Just awesomeness wrapped in an episode.
"Children of Time" was great to see the what-ifs and knowing that future Odo was willing to wipe them all out to save her was heart-breaking
"Trials and Tribble-ations" is when Jadzia Dax became my favorite character in Trek because with one conversation I could definitely relate to her. "Not Kirk, Spock!"
"His Way" when Odo and Kira finally kiss. Although this was yet another relationship drawn out, I think that it was done better than most and them getting together was hilarious and perfect for the personalities.
"Wrongs Darker Than Death or Night" I really thought Kira was going to kill her mother. It's an interesting perspective for a character that viewed anything related to Cardassians in terms of black and white
"Treachery, Faith, And the Great River" even though I was not a big Nog fan, I did love the way he so happily helped O'Brien with the concept of the "Great River" Not to mention the Odo supporting Weyoun kind of added to the sadness of the war. He just wanted to do the right thing and follow the god that represented his desire.
...and there are probably a whole lot more I just can't remember right now.
Voy.
"Blood Fever" only because it got the two together-ish. I still think it was one of the best couples of Trek until the writers rendered them lame. And no, I do not believe relationships must = death of chars.
"Before and After" was a sneak peek into what could have been an absolutely stellar season if they didn't drop the ball. The Year of Hell could have been an entire season of struggle and sacrifice and hardship as it should have been for a Federation ship flung across the galaxies.
"Living Witness" was a great story where the Doc had to cope not only with the fact that he was just a copy, but that the people he knew and loved were still alive but long gone with the original EMH and the stirring of a civil war on the planet where he was found. That's a lot for an ep.
"Blink of an Eye" because it was a great way to see how a more advanced culture could influence a less advanced culture without even communicating with them.
Just adding this now... "Muse" I just loved the way Voyager's stories were turned into plays.