Pound for pound, Doomsday Machine has the most great moments of any TOS episode. Several have already been mentioned. Gentlemen, I suggest you beam me aboard. The music in the episode is outstanding throughout the entire episode. Spock consoling Kirk on the death of his friend. Decker coming out of shock. I think it's great, Scotty get us out of here! I could continue, but you get the idea.
I also like the "forget" moment in Methuselah, but why didn't Spock make Kirk forget Edith Keeler?