I'll give a shout out for All Our Yesterdays, The Omega Glory and The Savage Curtain. The Ron Tracy character is very dramatic as a rogue captain who's gone crazy, a very evocative performance. The fight scene is good value for being suspenseful, keeps me on the edge of my seat. I like The Savage Curtain for a look at characters from ST's future history, an interesting look at Kahless.
My own personal favorite is Whom God's Destroy. The antics those insane people are fun and funny, and at the right moment can catch you off guard with flashes of dangerous darkness. Marta's fate was a particularly good shock, after laughing my way through her and Garth's quirky interaction with each other.
I'm also fascinated by the nature of Garth of Izar. From the standpoint of someone who likes to do creative writing, this is a character whose backstory is so intriguing to me, I feel like the character could be re-purposed to explore a different aspect of the ST universe. I like playing with the idea of Garth as someone who represents the dark side of learning about and internalizing alien cultures, ethics, and patterns of thought. The training he received from an alien culture to learn how to restructure himself effected his mind, changed it in unexpected ways. I like to imagine the character being used to explore how cultural relativism can go wrong.