I' getting in this late but...

The City On the Edge of Forever
Metemorphisis
Jouney to Babel (Prequeled on Enterprise)
Is There No Truth In Beauty?
The Trouble with Tribbles (revisited in anothe Star Trek series)
Space Seed

Two from STNG

I can't think of the episode name at the moment but it features Spocks Father Sareck who is slowly loosing his mental facalties and is aided by Jean-Luc.

"Inner Light" which has a haunting musical piece which I have heard since as an orchestral Suite that is great.

How about the movies? Your top ones.
Mine are:
The Wrath of Khan
First Contact
Insrurection (Love the humor)
The Voyage Home
An Undiscovered Country

(They're all good save perhaps the first but these are my favorites)

Bill