One of my all time favorites was "The Empath" - though it had very sparse sets, and few effects, it did get to explore just how close "The Big Three" were to each other, including how strongly (in a positive way) Spock felt towards McCoy (including him comforting McCoy while Kirk was fuming, and the "anger" beams surrounding him as strong or stronger than they did Kirk at the end).
And there's Doomsday... another favorite.
Oh, there are sooo many...
-Rob