Mystery Science Theater 3000 (often abbreviated as MST3K) is a television show which ran from 1988 until 1999, first airing on cable on the Comedy Channel (succeeded by Comedy Central in 1991) and later on Sci-Fi. Hosted by creator Joel Hodgson (and later by Mike Nelson), the science-fiction flavored series featured the sarcastic host and his two robot puppet sidekicks, Tom Servo and Crow T. Robot making fun of "cheesy movies" (mainly classic B-science fiction and horror films with the occasional barbarian epic, cop drama, or biker flick) by talking over the soundtracks. Over the run of the series, several references to the Muppets were made.
- Episode #301 - Cave Dwellers - Two men drink to the health of a blonde man's stay at their villiage. Joel supplies in a high pitch voice, "Champange makes me giggly." Tom and Joel give Miss Piggy's giggle.
- Episode #306 - Time of the Apes - Joel sees the opening credits and says it looks like a Sesame Street segment.
- Episode #319 - War of the Colossal Beast - Upon seeing the bald man at the Medical Research desk, Crow says "Fred Mertz?" to which Joel replies "More like Bunsen Honeydew."
- Episode #322 - Master Ninja 1 - Joel thinks that aged Lee Van Cleef looks like a Henson rat.
- Episode #403 - City Limits - Early in the film, a character yells out to another character named Ernie. Joel replies "yeah Bert?" in Ernie's voice. Ironically, the other character is actually named Bert. Joel repeats his Ernie imitation again later in the film.
- Episode #417 - Crash of the Moons - When a spaceship flies by the entire crew shouts "Pigs in Space!" Later in the episode, Servo quips that the villian is "The Count from Sesame Street."
- Episode #420 - The Human Duplicators - During a discussion of the missing Dr. Munson, Joel to calls out "Dr. Munson Honeydew!"
- Episode #421 - Monster A Go Go - Upon a tight, dark shot of the "monster" fumbling about, Joel imitates Cookie Monster's trademark "Coookieee" and munching sounds.
- Episode #512 - Mitchell - In this film starring Joe Don Baker, a skinny, bearded man is onscreen for a moment. Joel quips, "It's Jim Henson!" The robot puppet Tom Servo responds with an impersonation of Kermit, saying "Hi ho!"
- Episode #605 - Codename: Diamond-Head - A failed Hawaii Five-0-esque TV pilot, the reference is very similar to the one in #512, above, when one of the Coast Guard officers, who is also a skinny man with a beard appears on-screen.
- Episode #611 - Last of the Wild Horses - Crow: "He's the George Stephanopolous of the ranch." Tom Servo: "Snuffleupagus?" Mike: "George Snuffleupagus."
- Episode #614 - San Francisco International - Crow: "He's from the Land of Misfit Toys...a Henson rat!"
- Episode #703 - Deathstalker and the Warriors from Hell - Mike quips that the film's villian "looks like Sam the American Eagle."
- Episode #803 - The Mole People - someone holds up a pelt. Tom Servo says "They killed Fozzie Bear!"
- Episode #903 - The Pumaman - In one scene a man is jogging in the park in a bright yellow jogging suit, they respond by saying "The new Big Bird active wear!"
- Episode #908 - The Touch of Satan - Observer (aka Brain Guy) is made by Steffi, the babysitter to take his nap, and he asks for his "friend", a Cookie Monster doll.
- Episode #910 - The Final Sacrifice - a Canadian adventure/fantasy film, in one scene the teenage hero Troy McGregor is being chased by the villains' ski-mask wearing goons. Along the way, they crash over some garbage cans and Tom Servo sings in a Oscar the Grouch-voice "I Love...AHHHHHHHHHH".
- Episode #1001 - Soultaker - The female lead is seen at the hospital in a bed, with breathing apparatus attached to her nose and mouth, Mike Nelson says "She's Snuffleupagus!"
- Episode #1008 - Final Justice - Another Joe Don Baker film, one scene features a shot of a parade float that slightly resembles a scantily clad Miss Piggy. Tom Servo's impersonation: "Oh, Kermie, let me show you my good stuff!"
- Episode #1010 - It Lives By Night - Servo quips that the babbling, drunken drifter "sounds like the Swedish Chef Muppet."
Also, in Killer Shrews, when the shrew hid under the stairs, Joel screamed theres a Muppet under the stairs. And in Angel's Revenge, a bearded man hid behind a car, getting Tom to shot IT'S JIM HENSON! while the man shot at the heros, as Crow did his impression of Kermit's 'Hi-Ho!' and the man was shot, getting crow to shout in Kermit's voice. 'OW!"
- A running gag involved frequent references to "Jim Henson's [blank] Babies," alluding to Muppet Babies:
- Episode #403, City Limits, during one of her "action" scenes in the film, Joel calls out "Jim Henson's Rae Dawn Chong Babies." Later, when a brigade of scale-model fighter jets are shown, Crow quips "Jim Henson's Flying Leatherneck Babies."
- Episode #405, Being From Another Planet, Crow quips "Jim Henson's Baby Babies" upon seeing an infant in a crib.
- Episode #406, Attack of the Giant Leeches Servo refers to several characters as "Jim Henson's Cracker Babies."
- Episode #407, The Killer Shrews, included Joel's invention "Jim Henson's Edgar Winter Babies" (coincidentally, Edgar Winter was also born in Leland, Mississippi) and "Jim Henson's Last Picture Show Babies."
- Episode #420, The Human Duplicators, a stern-faced character causes Joel to call out "Jim Henson's Jack Palance Babies."
- One popular subject for the series was the 1964 Christmas oddity Santa Claus Conquers the Martians, co-starring Sesame Street cast member Bill McCutcheon as Dropo the martian.
- After leaving MST3K, Joel Hodgson and his brother Jim worked with The Jim Henson Company to produce a show for broadcast on Noggin. This never saw the light of day.