I seem to like all the unpopular episodes. From all series.
I luuuuuuuuurve Whom Gods Destroy I just find it so entertaining. I like the idea of the code it seem very James Bond and I find Garth hilarious (I may KILL you with my bare HANDS!!!!). Also like Spock's Brain and Omega Glory.
And I like Plato's Stepchildren (dun dun DAAAAH) (don't kill me). Mainly because this is the first thing of ANY Star Trek I ever saw (closely followed by Wink Of An Eye then Whom Gods Destroy (Love all these!). Also the kiss is a great moment.