What exactly were your criteria for TOS? I think this exercise is useful for the serialized style of DS9, but due to the episodic nature of TOS it becomes somewhat pointless. For instance how is a hackneyed racism plot like Battlefield, or a "Nazis in Space" episode, any more representative of the themes or characters of the series than random episodes like The Enemy Within or Charlie X? And how can something like Conscience of the King or Obsession be excluded when they provide valuable insight into Kirk's character, while Operation Annihilate!, which is only notable for establishing Spock's ridiculous inner eye lid and Kirk's trivial dead brother, is included?
And The Infinite Vulcan?!