The episode: “Track of the Moon Beast,” ep. 1007
The riff: Said in a silly voice by Mike as one of the movie’s protagonists, Paul, slowly (very slowly) transforms into a scary-looking lizard man.
The explanation: The lizard man in “Track of the Moon Beast” bears a pretty close resemblance, other than its color, to the famous “Gorn” alien from the “Arena” episode of Star Trek, the original series. “Arena” is one of the best-remembered episodes of the show, and deals with Kirk and a dangerous Gorn opponent being stranded on a desert planet by another powerful and enigmatic race called the Metrons, forced to fight to the death. Kirk soon realizes that in the Gorn, he’s up against a tremendously strong but slow/bulky opponent, and he eventually uses scientific know-how to win the day.
Novelty factor: Knew this one all the way. I still have never really seen a ton of Star Trek episodes, but this is one that just about any geeky guy has seen at some point, if he’s seen any of the original series at all.
MST3k Riff-a-Day 
This was also the episode where the Mythbusters got the idea for making gunpowder like Kirk did and building a cannon to shoot a cutout representation of the Gorn. 🙂
Yeah, I think pretty much any Star Trek fan would get this particular reference–not the most obscure overall, but a classic episode.
And it’s also also the episode that Bill & Ted are watching in “Bill & Ted’s Bogus Journey”, as well as the location where the Evil Robot Us’s kill Bill & Ted!!