Taste of Armageddon
I've always liked this episode, mainly for it's anti-war message, which still applicable today, probably even moreso. War is never clean, and all kinds of war just sucks. I loved Kirk in this episode, trying to make that point to Anon 7, and him showing how "Barbaric" he can be. I do kind of wish Fox wasn't such an imacile, but I guess he was portraying what a real politician would be like (I have low regard for politicians).
This Side of Paradise
The end of this episode reminded me a lot of the end of Taste of Armageddon, when Kirk was talking about that inner struggle to achieve and we don't deserve paradise. It's that sense of achievement and work and challenge that keeps us going in our lives, and that's a powerful message, and one of Trek's best. Also, Spock is such a heartless romantic.

On a serious note, it was great to see Nimoy get to have emotions and see that relationship with Layla, even if it was under the spore influence. Loved the scene with Kirk just insulting Spock and his race. Not a good idea to get a Vulcan (Or is it Vulcanian) mad.