1. The Visitor. I would argue this is the best Star Trek episode ever. Cried the first time I saw it, and upon each subsequent viewing.
2. Far Beyond the Stars. Avery Brooks is awesome in it. Confronts the ugliness of racism head-on.
3. In the Pale Moonlight. Never get tired of this one. Starfleet officers fabricating evidence in order to justify pulling the Romulans over to the losing side in a war. Again, Brooks at his best.