"Spock's Brain" more for the ice-covered planet (and set) which was rare on TOS.
I just love the rear projection on the bridge viewscreen, which was almost never done except this ep.
A PRIVATE LITTLE WAR is a mess of a show, but the ending really resonates for me, since they just up and LEAVE. SYMBIOSIS on TNG tried for the same, but it didn't succeed the same way.
Like WINK OF AN EYE for Kathie Browne and for Kirk actually being seen tugging his boots on 'after.' For 60s TV, that is practically like showing full-frontal.
Have a soft spot in my heart for SAVAGE CURTAIN, because seeing Lincoln on the viewscreen was, along with Kirk fighting Spock on Vulcan, my only memory of first-run TREK. Oddly enough, when TOS went into syndication in the bay area around 1972 or 73, they ran a special preview on a weekend night, probably during CREATURE FEATURES. I remember being very excited, but then saw ... Lincoln on the viewscreen! Part of me wondered if he was going to be in EVERY episode ...
THE EMPATH is my alltime favorite episode ... and the last new one I ever saw. Even though I saw ARENA 50 times in the 70s, I kept missing THE EMPATH, and didn't see it till I was practically out of high school, probably 77 or so. I think it is just beautiful, and it balances up my other faves, which are more traditional action (DOOMSDAY, IMMUNITY, BALANCE, ERRAND) and the fact I have a soft spot for all Ralph Senensky eps (he is easily my favorite trek director, everything he did was a winner IMO.)
And since it is the most like TOS ... I guess I should include TFF as another alltime favorite unpopular ep, since I like it even more than TMP, almost as much as TWOK, which are the only 3 trek movies I really really strongly enjoy.