No one is voting for the Space Hippies episode? Blasphemy!
My top 3 would be :
1) Balance of Terror - The whole "dueling commanders" plot was masterfully done. Considering how underutilized the Romulans have been in Star Trek lore, this was a great example of how similar Humans and Romulans are in the Star Trek Universe.
2) City on the Edge of Forever - See Buftex's great description.
3) The Doomsday Machine - A Moby Dick re-telling in the 23rd century. With spaceships.