I'm not sure what is the best one, but I have about 78 favorite episodes.
One of my absolute favorites is Balance of Terror.
The long running battle, which is action packed but also very well thought out with a lot of strategy, is excellent. I get tired of so many things where the overall strategy is drive right up to them and try not to blow up before they do.
Also, Mark Lenard is great as the Romulan Commander. He's the enemy, but he's not evil or cackling foil, he's someone we might have wanted to know as a friend if given different circumstances, he even feels the same and say so. Decius is kind of a jerk, though.
Two more things that make this one my especial favorite. I love the opening sequence where Kirk walks onto the bridge and everyone just reports to him without his saying a word. Everyone is doing their jobs and the whole crew is good at doing them, not just the captain. That's another one so many other things have failed, a captain who's a superhero with a bunch of drones is not how things really usually work.
I also like the reaction shots that happen through out the episode, but especially right after base 4 is destroyed. Even if someone didn't get a load of lines, they still got to react and emote a bit rather than being the back of a head in the viewscreen shot or set dressing while Kirk is speaking.
Actually, there's more, but I'm jamming up the thread.
