The control panel for the robotic arms that Mike uses to grab the Hubble is marked "Manos." Manos, along with being Spanish for "hands", is also a reference to the movie Manos: The Hands of Fate (1966) which is generally agreed to be the worst movie ever shown on Mystery Science Theater 3000.
The makers of Mystery Science Theater 3000 (1988) were so annoyed by their experiences having to work within a major studio on this film that they later parodied the experience on the TV series. In Mystery Science Theater 3000: The Incredible Melting Man (1996), the host segments are about Crow's screenplay being purchased by a studio then ruined by the executives (Dr. Forrester and Mother Forrester) as they vainly try to shoot it and screen it for audiences. Series writer and star Mary Jo Pehl would later call the episode an "exercise in healing" after the ordeal of MST3K: The Movie.
When Universal originally released the movie, they thought that a limited release in a select group of "college towns" (where they believed Mystery Science Theater 3000 (1988) was most appreciated) over a longer period of time would lead to a box office bonanza and keep it from having to compete with the early summer blockbusters like Twister (1996) and Mission: Impossible (1996). Instead, very few fans of the show were even aware that the movie had been released and the film languished in relative obscurity throughout the spring and early summer. This was the first (and last) time that Universal attempted such a plan.
By many accounts, making the movie was not a happy experience for the filmmakers, due to frequent studio interference. Years later, at a cast reunion appearance in New York City, Trace Beaulieu was asked what the worst movie featured on MST3K was. His reply was, "Mystery Science Theater 3000: The Movie".
When Mike Nelson uses the manipulator arms to free the Hubble, not only does the panel say Manos (see above), but when he clicks the button we hear a subtle reworking of Torgo's theme. Torgo was the central character of Manos, The Hands Of Fate and Mike Nelson would often make cameos spoofing Torgo throughout the shows' existence prior to his taking over from Joel Hodgson (the show's creator and star for 4 and a half seasons).
At one point, Crow quips, "Oh, PLEASE, let us get the Sci-Fi Channel, oh please, oh please, oh please!" At the time, the production company Best Brains was negotiating a deal to air on the Sci-Fi Channel.
Tom Servo says, "Oh, they're flying into a Roger Dean album cover." Roger Dean designed many of Yes's album covers, starting with 1972's "Fragile," many of which look like the scene in This Island Earth (1955) that Mike and the bots were watching at the time.
The original DVD release had no special features and was withdrawn from circulation in 2000. However in 2003 on the 7th anniversary of the movie's premiere (19 April 1996) an unknown Internet fan released a Special Edition DVD. This two disc set has the widescreen version of the film, the theatrical trailer, TV spots, a review from E!, a slideshow presentation from the 1996 MST3K convention and the cut host segment & alternate ending.
The "hard copy of the status report" that Mike is reading at the beginning of the film is actually a copy of "Satellite News" the official newsletter of the Mystery Science Theater 3000 information club.
Most of the puppeteering for Gypsy was actually done by Patrick Brantseg (who would later take over both the puppeteering and voice in the TV series) and the voice was dubbed in later by Jim Mallon. This was so Mallon could focus on directing the scene rather than operating the puppet.
The German version of Mystery Science Theater 3000 (1988) was translated by the German TV comedian Oliver Kalkofe. Many jokes were changed to jokes about German tv shows and stars. Kalkofe even added some new jokes.
In the scene in Tom Servo's bedroom, to the left of the interocitor, is Tom Servo's portrait of his "Ideal family" (Haley Mills, Peggy Cass and Gigantor) from the television series episode "I Accuse My Parents."