Errand of Mercy
is one of my favorite episodes. The story has an interesting moral lesson and Kor is a great villain. However I have also felt that there was something intrinsically wrong with the plot-line. Specifically, I never understood why the Organians remained silent about their true nature (and their subsequent invincibility) until the very end of the episode.
I realize that it would have been a very short episode had they simply explained to Kirk from the beginning why they really were not at any risk, but it would have made more sense from the Organians point of view if they had. Why would the Organians want to string them along? Surely they must have realized that Kirk just wasn't getting it, so why weren't they more explicit from the get-go?