The Enemy Within
Where it should have been: #34, so another middle-of-the-road episode.
In case you forgot: Good Kirk and Evil Kirk run around the Enterprise while Sulu and an anonymous landing party almost freeze to death on the planet below.
Serious ethical dilemmas and meditations on the greater philosophical point about the duality of man are the kind of heady stuff that makes Trek stand out from the other pulp of its time. Even if it doesn't really dig that deep into the questions, it's nice that they even bothered to ask. Sulu's deadpan lines are great and probably the highlight of the episode; it's not much, but it does reveal a certain amount of stalwart, stoic courage he doesn't often get to display up on the bridge.
I also just love that goofy little space dog. TOS could have used some more costumed animals.
I enjoyed "The Enemy Within" a lot the first time I watched it, but a second viewing soured much of it. Poor Yeoman Rand didn't have much purpose in her few episodes except to bring food to Kirk and to be menaced/assaulted as the script called for. The pacing also drags: they figure out fairly early on that the transporter is duplicating things into Good and Evil (though it seems like Passive and Aggressive would have been better descriptors), but it still feels like it takes everyone much longer than is necessary to solve the freaking problem. Evil Kirk has to accidentally phaser some of the components of the transporter (in the engine room...?) to stretch the episode out even more and give it a bit of extra dramatic tension.