- In "Valerie 23", the android title character tells Frank Hellner that she is "fully functional" when it comes to sex. In the sequel episode "Mary 25", Charlie Bouton asks the android of the same name if the same is true of her and regularly has sex with her as the episode progresses. This refers to the Star Trek: The Next Generation episode "The Naked Now" in which Tasha Yar, suffering from the Psi 2000 virus, asks Data if he is fully functional.
- In "Hearts and Minds", the vital energy source which the soldiers are trying to protect is called pergium, a reference to the radioactive element of the same name being mined on Janus VI in the Star Trek: The Original Series episode "The Devil in the Dark". "Hearts and Minds" was written by Star Trek screenwriter Naren Shankar.
- There is also one to Starship Troopers in "Hearts and Minds" as the human soldiers are (seemingly) fighting an insectoid alien species whom they refer to as "Bugs."
- "Rite of Passage" features a dog in a post-apocalyptic setting who is (incorrectly) believed to be telepathic, in reference to the telepathic dog Blood in A Boy and His Dog.
- In "Mary 25", Charlie Bouton says that the title character was "named after the famous nanny from the movies."
- In "Nightmare", there is another to the Star Trek franchise as there is mention of the Starfleet Research Lab in Fort Dix.
- In "The Human Factor", Commander Ellis Ward and the android Link play a game of chess to determine whether humanity deserves to exist, in reference to The Seventh Seal.
- Also in "The Human Factor", Link has yellow eyes, much like Data in Star Trek: The Next Generation.
- In "Music of the Spheres", Vic's nickname for Devon Taylor is "Doogie."
- In "Better Luck Next Time", the aliens are named Gerard and Kimble and claim they have been endlessly chasing each other, a reference to the main characters of The Fugitive.
- Also in "Better Luck Next Time", Russo, LaRue, Daniels and Esterhaus are all named after characters from Hill Street Blues.
- In "I, Robot", Adam Link was built at the Rossom Hall Robotics Laboratory, a reference to the 1920 Czech play R.U.R. by Karel Čapek which introduced the word "robot" to science fiction and the English language. The robots in the play (who are really Artificial Humans) were created by Rossum's Universal Robots.
- In "Déjà Vu", Corporal Hanford is running a betting pool on the likely (and unlikely) outcomes of the teleportation experiment. One of the options is "The Fly".
- In "Skin Deep", Sid Camden has the poster for The Body Snatcher above his mantelpiece. This is a reference to the fact that Sid imitates Chad Warner using a Holographic Disguise and eventually kills him so that he can take over his life permanently.
- There are numerous references to 1984 in "Stasis". The episode depicts a Dystopia in which society is divided between the Elite and the workers with the former essentially being the Inner Party and the Outer Party combined and the workers being the Proles. Winston is named after the novel's protagonist Winston Smith.
- In "Down to Earth", Dale LaRose refers to Ceti Alpha V. This was the planet where Captain Kirk marooned Khan Noonien Singh and his followers in the Star Trek: The Original Series episode "Space Seed", as later seen in Star Trek II: The Wrath of Khan.
- In "Abaddon", the interplanetary hauling vehicle Pequod is named after the whaling ship from Moby-Dick.
- In "The Origin of Species", there is one to Planet of the Apes (1968). Hope and the six students initally believe that the ship has brought them to another planet but they realize that they are on Earth in the future when they find the ruins of the Golden Gate Bridge.
- In "Sandkings", Dr. Simon Kress says, "Charlton Heston, eat your heart out!" when the Sandkings part into two groups in front of him. This is a reference to Moses parting the Red Sea in The Ten Commandments. When this scene was later shown in the Clip Show "Final Appeal", the relevant line was cut to avoid a case of Celebrity Paradox as Heston played Chief Justice Haden Wainwright in that episode.
- In "Family Values", when Jerry Miller asks Gideon Robotics to take back his household robot Gideon, the robot running the company says, "I'm afraid I can't do that."
- In "Patient Zero", Colonel Beckett is sent back in time to 2001 to prevent the outbreak of the Gehenna Strain. This is a reference to Quantum Leap and the efforts of another time traveler, Dr. Samuel Beckett, to change history for the better.
- In "Zig Zag", many of the characters are named after famous Major League Baseball players, Tinkers, Chance, Yaztremski, Stottlemeyer and Mickey.
Shout Out / The Outer Limits (1995)