#2: The Changeling
In case you forgot: The Enterprise has run across a deranged space probe that's intent on sterilizing the entire galaxy. Fortunately, it thinks Kirk is its creator, buying everyone some time until Kirk eventually out-logics it into self-destruct land.
The good: Hands-down the best "man versus machine" episode of them all. It doesn't matter that computers and artificial intelligence don't really work that way; the story is good enough otherwise that I'm more than willing to accept Nomad's accident as a necessary plot contrivance. The threat builds nicely over the episode, and when Kirk outbrains the probe, it's well-earned, not as deus ex machina-y as the Kirk versus the computer episodes can sometimes get.
The bad: Uhurua's "knowledge wipe" is freaky. Obviously TOS is episodic and so she's back to normal next week like nothing ever happened, but the implications of what a knowledge wipe would entail and what it would do to a person are pretty heavy. I think it would involve more than just teaching her to read again.