My personal favorite is the final talk between the Romulan Commander and Kirk in the "Balance of Terror' It was the finale to a wonderful battle of wills and strategy. The final nod of respect the commander gives to Kirk :
Romulan Commander: I regret that we meet in this way. You and I are of a kind. In a different reality, I could have called you friend.
added with the final sad note concerning the death of Lt. Tomlinson and the woman he almost married Ens. Angela Martine...concerning the price of such war that might have occured on a grander scale had the Bird of Prey reach its home port, as the Romulan Commander feared.
I would say the look on the miner's face and the reversal of their fear and hatred as they learn they had been innocently killing baby hortas and that they were the monsters was a close second for me. What started out as the scariest TOS episode for me as a kid, actually had a bright hopeful end...