TOS: Balance of Terror (1.09; Season 1)
This one had everything -- space battles, high drama, loss and sorrow, and an enemy worth fighting. When I saw Serenity, I saw shades of the Romulan Commander in The Operative -- it wasn't that the commander hated the Federation... he was just doing his duty, and if that involved destroying the Enterprise, so be it. The commander influenced every Romulan that came after him.
TNG: Frame of Mind (E147; P247; Season 6)
I really never liked Commander Riker. I never thought he grew very much as a character. But Jonathan Frakes really pulled this off well, and made the episode work. Brannon Braga wrote a lot of great episodes (which leads me to believe that it was Rick Berman's influence that made him evil).
TNG: Parallels (E163; P263; Season 7)
Hey, look, another Braga episode! I liked this episode more for the parallel universes than anything else. The mystery of how things kept changing was secondary. Many Star Trek fans like thinking about "what if x had happened instead of y?" This episode addresses that and keeps it exciting.
DS9: Starship Down (E78; P479; Season 4)
When you want to destroy things, the first person you turn to should be David Mack. This is a great ensemble episode reminiscent of TNG's "Disaster", where everyone has to work together toward the same goal without knowing if people on other parts of the ship are doing the same. Plus, I like the emotion Nana Visitor shows when she's afraid Sisko will die.
VOY: Living Witness (E90, P191; Season 4)
As a whole, Voyager isn't a bad show, cast in the mold of TOS, but by now we need more than TOS to keep our brains occupied. This episode is another alternate-reality one, cowritten by (guess who!) Brannon Braga. The Doctor got to be an annoying character sometimes, but in this episode it's not so bad.
ENT: I couldn't think of any episodes I really liked. *shrug* The Terra Prime arc was decent.