This was difficult, but I think I narrowed my list down to five (sort of)

5. Journey To Babel/The Savage Curtain
I couldn't make a decision of which episode to leave off. I love that Curtain has the various famous leaders of various cultures, the other has Spock's parents, I just can't make a decision.

4. Amok Time
Come on, we all after reading that have the fight music in our head.

3. The Naked Time
Come on, crazy Sulu running around the Bridge with a sword? Classic

2. City On The Edge of Forever
This may be the episode the grips you the most emotionally in the entire original series.

1. Space Seed
He was a king once...with POWER over MILLIONS.

One that should get a HUGE nod in the meaning behind it is Let That Be Your Last Battlefield, it's so true with our nature it's a frightening mirror.

Anyone else miss Mudd?