The Menagerie with Captain Pike in the blinking wheelchair. He was creepy. And then there was The Doomsday Machine with the music that played over, and over, and over whenever they did a shot of the planet-destroying-club-of-glowy-doom. My favorite episode though, The Best Episode Ever, is The Trouble with Tribbles and here's why.
Tribbles not only look cute, they sound cute. If they're happy, then they purr, just like a cat but without the claws or annoying hairballs. And as an added bonus they also function as a Klingon early detection system. Tribbles are awesome. If not for Tribbles then who knows how many innocent civilians would have been killed after making a loaf of bread out of poisoned quadrotriticale? And how else would Kirk (all hail the Best Captain Ever) have known of the Klingon treachery? Even he would have been stuck trying to figure out who had perpetrated such a heinous crime. If not for the Tribbles and their insistent squeaks then the evil Klingon agent would have gone undiscovered and continued to cause trouble for The Federation.
This episode also features the most fantastic bar brawl in all of Star Trek history. It's better than the one in The Next Generation when Picard nearly gets killed. Better even than the countless brawls in Quark's on Deep Space Nine. Why? Because this brawl doesn't start over a woman, or a peace treaty, or a cardgame. It starts because the Klingons, after tossing out insults against humans and even Captain Kirk, make the mistake of insulting the USS Enterprise in Scotty's presence. This is the last straw for the Chief Engineer who then knocks out the offending Klingon with the first punch of this Epic Brawl. There you have it. Tribbles saving the day and Scotty protecting his ship's honor. The Trouble with Tribbles is the best Star Trek episode, ever. If you think a different episode is the Best Ever, by all means try to prove me wrong with your comments. I love a good Geek Fight!