"Amok Time" is apparently the first episodes to feature "Live long and prosper" as well as the Vulcan "V" hand salute. Also according to Wikipedia, Sturgeon came up with the Prime Directive in an unused Star Trek script.

But I was surprised to read about this subtle moment in "Shore Leave" when Kirk thinks that Spock is giving him a back rub and is surprised and apparently disappointed to find out that a female officer has her hands on him.

I used to know "Shore Leave" and "A Taste of Armageddon" practically by heart since I had them on audio tape and used to listen to them over and over. I didn't remember this from "Shore Leave" and didn't think I could have missed something like that but sure enough, there it is.