Is There In Truth No Beauty? While the fact that Dr. Jones couldn't make a mind leak after working with the medusan for so long and Spock being able to immediately seemed a little implausible, it was a brilliantly written episode in my opinion that examined a really interesting style of human prejudice.
The Cloud Minders--- The Spock/Droxine thing was not good at all but it was another great episode in the way it looked at class and the fact that it explored how a seemingly utopian society usually does exist thanks to the suffering of others. I thought it actually served as an allegory for the slavery-era south. Also, I really liked the Vanna character. Yeah, she did some things that were really sucky, but you kind of sympathized with her and understood her motivations. And she was a bad-ass. In my mind she served as a perfect anti-hero.
Actually, now that I think about it, the issue of social class popped up quite a bit in the third season, which I think was its saving grace.
Plato's Stepchildren: There was a lot of dramatic tension there. They did it really, really well if you ask me. And it explored class relations in a more subdued way.
Let That Be Your Last Battlefield: Once again, interesting analysis of social problems.
The Savage Curtain: A great exploration of ethics.
Day of the Dove: Your basic demon-possession plot, but in space. I think it translated really well.