"Plato's Stepchildren", for themes of equality and justice,
The one where Kirk, Spock, and McCoy all get captured on a Roman-era island, for themes of liberty
"Omega Glory", because I'm just that American, and finally,
"Mudd's Women", for themes of inner beauty and human rights. But my absolute favorite hated-on episode will always be:
"The Empath". So many GREAT character moments in that one; you really felt the love that the Big 3 all had for each other. It also explored the themes of compassion, selflessness, and what a person will do to save the who he/she loves.