#8: The Devil in the Dark
In case you forgot: Kirk and Spock team up against a silicon-based life form called a horta that's wreaking havoc on Janus VI, a mining colony. Turns out the horta holds no animosity towards the miners per se, but rather is just doing the best it can to protect its eggs, a huge number of which the miners accidentally destroyed.
"The Devil in the Dark" has a solid science fiction premise, an intriguing mystery going on for the first half of the episode or so, and a graceful, optimistic ending. Personally, what I like the best about it isn't that the threat isn't an obvious an easy analogue to FOREIGN POWERS or what have you; instead of Klingons or Romulans or some new alien race that inexplicably speaks English, it is a being that humans are incapable of communicating with or relating to. (Sound familiar?) Fortunately Spock's around to work a little mind-melding magic and we get the full picture.
It's a nice little fantasy to think that every bad guy you've read about in the papers or seen on the news is an objectively bad person who truly delights in evil, and sometimes it may even be true. But more often than not, it's a group of people who are just doing what they feel is the right thing, or at least the thing that has to be done to protect themselves. Accommodating them may tax our abilities to the utmost degree, but it's taking that noble path that represents the best parts of humanity.
(Shatner lists this as one of his favorite episodes, incidentally.)
You have to wonder just how willing the miners would be to peacefully coexist with the horta if they weren't getting very convenient, pre-dug tunnels out of the deal.