1-4 are not only my favourite eps from season 3, they are my favourite from the whole TOS.
1. Is There in Truth No Beauty? (odd one and essence of the whole series at the same time)
2. All Our Yesterdays (beautiful and poetic like the first. It's a pity Aroeste didn't write more)
3. The Enterprise Incident
4. Spectre of the Gun (these two episodes don't seem old-fashioned even now)
5. Plato's Stepchildren (if Is There in Truth No Beauty is essence of TOS, this one is essence of the third season for me. Weird, creepy, decadent, colorful, campy and having too much emotional power - but that power really works here)
Honorable mention: The Way to Eden and The Cloud Minders.