This might be controversial, but it's all about your personal preference. What single episode do you think is the best one from each season?
For me (even though it changes from year to year, depending on my mood);
Season 1; Where No Man Has Gone Before
Season 2; The Doomsday Machine
Season 3; The Tholian Web
For me at this time:
Season One: City On The Edge Of Forever
Season Two: Catspaw
Season Three: Spectre Of The Gun