Mystery Science Theater 3000 (or MST3K) has made many references to Star Trek. Tom Servo's Used Robots, named for the cynical robot Tom Servo, was an in-joke added to the Promenade set decoration for Star Trek: Deep Space Nine.
"Last of the Wild Horses"
One episode in particular, "Last of the Wild Horses", spoofs the episode TOS: "Mirror, Mirror". The evil mad scientist Dr. Forrester attempts a matter transference experiment during an ion storm, switching the robots Tom Servo and Gypsy with their mirror counterparts. They find themselves in the mad scientists' lair, Deep 13, with an Evil Mike Nelson sporting a goatee beard and an evil robot Crow. Dr. Forrester and TV's Frank are nice in this universe and are subjected to watch bad movies on the Satellite of Love, or SOL. Evil Mike tries to discipline Evil Crow with his agonizer, but the batteries are dead, and the agony booth is out of order. Meanwhile, the Evil Servo and Gypsy are on the real SOL. Evil Servo pulls a dagger on Mike to take control of the SOL. Evil Gypsy seduces Evil Servo, to be his "captain's woman". The real Gypsy and Servo ask the mirror universe computer how to return things to normal and eventually do. The real mad scientists enjoy the agony booth a little too much. Many lines of dialog are lifted directly from "Mirror, Mirror" as well. In addition, there is a modified Terran Empire logo on Evil Servo's upper body, with the SOL through the Earth.
In the introductory host segment of an earlier episode, "Swamp Diamonds", Crow and Servo become obsessed with the episode TOS: "This Side of Paradise" (which Joel calls "the Elias Sandoval episode"). Crow dangles upside-down like Spock, Tom impersonates Leila Kalomi, and Joel imitates Kirk angering Spock to make the 'bots snap out of it, saying "Your father was a computer and your mother was an encyclopedia!"
"Danger!! Death Ray"
In the episode "The Skydivers", Tom Servo is giving a presentation on space when Crow interrupts him repeatedly to make jokes about Uranus, including that they have to "get to Uranus and wipe out the Klingons." In the same episode, they remark that a character has "teeth like a Ferengi."
"The Final Sacrifice"
In "The Final Sacrifice", the main character is reading a letter and Mike pretends that he's reading "Dear Counselor Troi: I waited at Denny's, but you didn't meet me."
"Prince of Space"
In "Prince of Space", Mike says "Make it BKAWK" (chicken sound) when the chicken-looking Phantom of Krankor gives an order.
"Horror of Party Beach"
Mike and the Bots remark that one of the girls is a Romulan.
"Overdrawn at the Memory Bank"
Crow remarks that the memory-holding "identicube" looks like, "Christmas on the Borg ship".
The final Comedy Central-era episode of Mystery Science Theater 3000 features the crew of the SOL adrift in space. All seems normal until they encounter a black hole, a terrified Crow and Tom call to Mike for help. Mike enters, however he is dressed as, and talking like, Captain Janeway from Star Trek: Voyager. After saving the satellite from the black hole (addressing Tom Servo and Crow as "Mr. Servo" and "Mr. Crow", another nod to Janeway) he celebrates by singing the song Proud Mary, from which Crow and Servo flee in terror. That episode also features a spoof of the perfection-loving Nomad called "Monad." As in TOS: "The Changeling", the robot is defeated when he is ejected into space. During the heckling of the movie (which was "Laserblast" which featured TOS-era sound effects as well as a score co-written by Joel Goldsmith) one of the cast quotes a line from TOS: "The Savage Curtain".
"Agent for H.A.R.M"
In the episode "Agent for H.A.R.M", Mike was placed on trial for blowing up three planets. The judge used language similar to Q in "Encounter at Farpoint", calling Humanity a "savage" and "child-like" species. Furthermore, Mike believed that he was on trial for all of Humanity but was, in reality on trial for himself.
"Pearl! Pearl! Hello? Our wessel is malfunctioning!" Mike is imitating Walter Koenig's faux-Russian accented Pavel Chekov, in particular one memorable scene from Star Trek IV: The Voyage Home.
"Wheeling Captain Pike down the hall!" is a reference to TOS: "The Menagerie, Part I" and "The Menagerie, Part II", in which Christopher Pike, the former captain of the Enterprise, was shown confined to a futuristic wheelchair.
"Parts: The Clonus Horror"
"Bride of the Monster"
"I'm dead, Jim". is a reference to Leonard "Bones" McCoy from The Original Series", who often had to remark (mostly about crew in red shirts) "He's dead, Jim".
"The Sword and the Dragon"
"Did you hear Kute Mulgrew is Mrs. Picard?" Kate Mulgrew is the actress who played Captain Janeway on Star Trek: Voyager. Captain of the Enterprise Jean-luc Picard frequently joins her in fan-fiction. In addition, Mulgrew played the previously unseen Mrs. Columbo in a short lived spin-off of that title.
"The Thing That Couldn't Die"
"They've beamed onto the planet O.K. Corral!" is a reference to TOS: "Spectre of the Gun", in which Kirk trespasses on the territory of the Melkotians and he, Spock, Dr. McCoy, Chief Engineer Montgomery Scott, and navigator Pavel Chekhov are imprisoned in an illusion of Tombstone, Arizona on the day that the Earps and Doc Holliday shot the Clanton gang at the O.K. Corral.
"The Crawling Hand"
"I think he's taken acting lessons from William Shatner" is said whenever a character overacts.
"No, I think she's doing Mrs. Captain Kirk!" Crow is comparing the land lady being strangled to possibly a scene in the film Star Trek V: The Final Frontier, in which Captain Kirk (William Shatner) is being strangled by the character Sybok (Laurence Luckinbill).
"Must think, Must Get back to Galileo-7..." Joel is starting up the segment by making light (once again) of actor William Shatner's delivery of lines. The hand theme, is most likely a reference to the fifth Star Trek film, Star Trek V: The Final Frontier. He mentions something called "Galileo Seven", which was a shuttle that the crew of the Enterprise discovered in Season 1 Episode 18 of the original Star Trek, titled "The Galileo Seven".
"Must cut transponder from wrist and fashion crude phaser device from..." Crow, also hamming up Shatner, is referring to a cliche of the Star Trek series where somebody in a position of peril would be able to build a crude phaser out of objects around them.
"...Must find pastel colored native female, and initiate the Prime Directive..." Tom's comment about "pastel colored natives" is reference to the Orion slave girls which were aliens with green skin, first seen in TOS: "The Cage". The Prime Directive is another Star Trek reference, a code of the United Federation of Planets, forbidding interference with the affairs of an alien world.
"I don't know how Shatner does it every week..." Joel is once more referring to actor William Shatner.
Mystery Science Theater 3000: The Movie
During the opening credits of This Island Earth, Servo comments "Space... the final frontier... These are the voyages of... Babylon 5."
While the list of actors in This Island Earth is being displayed, Servo states "Ok, lets see here... Shatner... Shatner? Nope doesn't look like he's in this one. We're safe."
When the airplane is being pulled into the flying saucer, one of the hecklers impersonates Sulu while saying "Captain, the Klingons have us in their tractor beam." Later as the spacecraft is flying, one of the bots continues his Sulu impersonation by saying, "There's a shuttle craft approaching captain. Do you want me to talk like George Takei some more Mike?"
As the space ship is landing on Metaluna, Servo states, "Remember we are parked in the Denubian Slime Devil lot."
On the return trip to Earth, Crow says the following: "Captain's Log: A bunch of our ship fell off and... nobody likes me." Upon entering Earth's atmosphere Crow continues his Shatner impersonation "Captain's Log: I've lost my toupee and girdle and I can't leave my room."
As Exeter is dying, one of the hecklers yells out "Spooooocccckkkk" in a Shatner style of overacting.
During the Sci-Fi Channel era, MST3K also had many allusions to Star Trek. The recurring character Observer (Brain Guy) and his species may have been a reference to the Talosians, the Q, or the Providers (since they were highly evolved, omnipotent beings, that were simply just brains, whose "bodies" were just illusions).
Also, throughout various latter year episodes, the Nanite characters (which had all been referenced in one Trek show at one time or another) were featured on certain occasions.(citation needed • edit)
Mike Nelson and Kevin Murphy (the voice of Tom Servo) provided an MST3K-styled commentary track for Star Trek V: The Final Frontier. Murphy called it Star Trek V: Shatner Ruins the Franchise. Nelson and Murphy, along with Bill Corbett (the voice of Crow T. Robot) also did a RiffTrax commentary for Star Trek VI: The Undiscovered Country, and Nelson and Murphy riffed Star Trek Generations. Nelson, Murphy and Corbett together riffed Star Trek, also, releasing it the day it came out on video. These commentaries can be purchased and downloaded from the RiffTrax website in MP3 format.