(written from a Production point of view)
Over the years, Star Trek's position as a cultural icon has resulted in many parodies and pop culture references of it on other television shows and movies. While some have been subtle tip-of-the-hat references, others have been complete copies, with the intention to reference Star Trek. Additionally, many small acknowledgments may not warrant inclusion, such as the use of the TOS transporter sound for various shrink rays, teleporters, etc. on SpongeBob SquarePants.
Produced by ATOZ Films in the 1980s, this white-trash parody of Star Trek II: The Wrath of Khan played at conventions for years until a "Special Edition" version, with added effects, was released on video in 1999. In the film, the Redneck Federation Starship RSS Bovine battles spacefaring cats.
Video parodies and pop culture references that originated online. Web comics can be found under literature.
Google Calendar uses stardates based upon the ideas of Andrew Main. Each day covers 5.00 stardates, 10000 stardates (2000 days) make up an "issue". Issue numbers are prefixed in brackets. TOS was issue , 0000 was January 4, 2162, (when he speculated the Federation was founded) and issue [-28] started in 2008.
A series of short comedy sketches by Funny Or Die spoofing the TV show Mad Men by transplanting it into present-day South Boston.
Star Track: Idomo , formerly Star Track: The Next Hesitation, is a web series that takes a satirical approach to expanding on the Star Trek universe. Produced in Montreal, Quebec, it is one of the only known Star Trek fan films to be produced regularly in Canada. Episodes are released at a rate of one per year.
Star Trek (France)
Comité de la Claque is a french group who began on web. En 2012 France 4 channel TV broadcasts their parody in Comité du Ciné show, on january 27th before prime time:
Steam Trek  is an online parody of the original Star Trek. The premise is a conception of how the original Star Trek might have been produced by George Melies, a hundred years ago, at the dawn of silent films. The "distant future" is taken to be 1980, and the USS Isambard is steam-powered with coal fuel.
Stone Trek  is an online animated parody of the original Star Trek. The premise is basically Star Trek meshed with The Flintstones, featuring a 1960s styled laugh track, and Hanna-Barbera sound effects. The series follows the adventures of the crew of the USS Magnetize. The show keeps count of how many redshirts end up getting killed in the episodes. The show also parodied the plot of Star Wars: Episode I: The Phantom Menace, with the Magnetize having to save Queen Armadillo from the Fashion Police.
Star Truc(k)  is a french parody of the original Star Trek.
Yu-Gi-Oh! The Abridged Series
- In the episode "Card Wars" of Yu-Gi-Oh! The Abridged Series, the characters make frequent references to the Star Wars series, prompting Tristen Taylor to ask, "What's with all the Star Trek quotes?"
Back to the Future: The Game
Episode 1 of Back to the Future: The Game has Marty pretending to be from the patent office in order to get a younger version of Emmett Brown (resident of 1931) to build a rocket drill. He threatens to award the patent to a Dr. McCoy if Emmett doesn't produce immediate results. The game also features voice work from Christopher Lloyd (reprising his role as the older Emmett Brown) and Roger Jackson. Coincidentally, the elder Doc Brown during his stay in 1931, takes the alias Carl Sagan.
Final Fantasy games
The first airship the player acquires in the video games Final Fantasy III and Final Fantasy IV is called Enterprise.
In one confrontation, Commander Shepard tells a krogan soldier that the ruins they're in are collapsing around them and will kill them all. The krogan responds, "Yes! Exhilirating, isn't it?", a direct reference to Kruge's response to Kirk's similar concern in Star Trek III: The Search for Spock.
Also, the game featured Marina Sirtis, Armin Shimerman, and Carolyn Seymour in various roles. Michael Dorn lends his voice to Mass Effect 2 as a krogan, a species with a warrior mentality similar to klingons.
Coincidentally, the commanding officer at the beginning of the game is named David Anderson.
In Mass Effect 2, when Commander Shepard visits a bar in the Citadel, his response to an alien drink served is "This is...it's green?". Similar lines are said about beverages in the episodes By Any Other Name and Relics.
Mortal Kombat games
In Mortal Kombat vs. DC Universe, Captain Marvel tells Superman, Deathstroke the Terminator and the Joker that their enemy is called Dark Kahn. Joker replies with a Kirk-like "KHAAAAAAAAAAAAN!!!" with appropriate echoes. When Joker is finished, Deathstroke promptly tells him to shut up.
Quest for Glory 2
In the Quest for Glory 2 introduction, the Enterprise-D is clearly seen in the sky and warps away seconds later.
A late chapter in the PS2 game Rogue Galaxy is entitled "All Good Things..."
A possible unit conversation for a Terran medic is "state the nature of your medical emergency". In one of the humorous taunts, the medic can say "He's dead, Jim".
In the PS2 game Spongebob: the Battle for Bikini Bottom, the mermalair level's boss is named Prawn. Dialogue with Mermaidman and Prawn leads Mermaidman to drop to his knees and yell, "PRAAAAAAAAAAAWN!!!" and is even true to the angle from the movie.
Star Wars games
A side quest in the video game Star Wars: Knights of the Old Republic is called The Trouble with Gizka, a possible reference to "The Trouble with Tribbles" (the gizka share the tribbles' considerable ability of rapid reproduction). The game also shares many aesthetic similarities to Star Trek and non-Star Wars sci-fi.
In Unreal 2: The Awakening, Aida is stated to be a master of three-dimensional chess. A board identical to those seen in Star Trek is present in her quarters.
World of Warcraft
The various teleporter operators in WoW are named after Star Trek engineers: "Scooty" (Scotty), "Jhordy Lapforge" (Geordi La Forge), and "Smiles O'Byron" (Miles O'Brien, or possibly his mirror counterpart "Smiley")
Other parodies and references
- Former Mystery Science Theater 3000 co-stars Mike Nelson, Bill Corbett and Kevin Murphy recorded audio commentary tracks mocking Star Trek V: The Final Frontier, Star Trek VI: The Undiscovered Country and Star Trek Generations. The commentaries were made available as an Internet-only download through Nelson's RiffTrax service. Recently, they've also released a track for Star Trek as well.
- Stand up comics have also been known to reference Star Trek as part of their acts. Bill Bailey has pointed out how his microphone makes him look like a Klingon motivational speaker, and Eddie Izzard has a routine of how the crew of the Enterprise could defeat enemies with different phaser settings. Two such examples are the 'depression', and 'I've left the oven on' settings.
- At the Rally to Restore Sanity and/or Fear on 30 October 2010, Jon Stewart used the imaginary threat of "corbomite" in bottled water to illustrate how media figures (personified by Stephen Colbert) create and magnify fears in the public. "You just got scared by something that is not real," Stewart said. After explaining the reference to "The Corbomite Maneuver", Stewart and Colbert briefly discussed Uhura's incongruous uniform in that episode.
- The Google Doodle of September 7, 2012 was an interactive homage to Star Trek: The Original Series. By continually clicking on it, the viewer could watch 'Kirk' and a redshirt reenact ""Arena"".
I'm a doctor, not a...
- Dr. McCoy (as played by Dan Aykroyd): "I'm a doctor, not a tailor, dammit." (The Last Voyage of the Enterprise)
- Dr. McCoy (as played by Phil Hartman in response to William Shatner (as Kirk) stating someone needs medical attention): "Dammit Jim, I'm a doctor, not a - oh, sure!" (Star Trek V: The Restaurant Enterprise)
- Doctor Cottle: "I'm a doctor, not a Viper pilot!" (Battlestar Galactica)
- Tolin Dorden: "I'm a medic, not a soldier!" (Gaunt's Ghosts)
- DeForest Kelley: "I'm not a doctor, I'm a convicted murderer." (Rowan & Martin's Laugh-In)
- DeForest Kelley: "How should I know? I'm an actor, not a doctor." (a commercial for Trivial Pursuit)
- Star Trek t-shirt: "Dammit Jim, I'm not a doctor, I just play one on TV" 
- Dr. Helena Russell: "I'm a doctor, John, not a miracle worker!" (Space: 1999)
- Wreck-Gar: "I'm a doctor, not a forklift." (Transformers)
- HK-47: "Dammit master, I am an assassin droid, not a dictionary!" (Star Wars: Knights of the Old Republic)
- Todo 360: "I am a Techno-service droid, not a butler droid!" (Star Wars: The Clone Wars)
- Ace Ventura: "For God sake, Jim, I'm a doctor, not a pool man." (Ace Ventura: Pet Detective)
- Dr. Carson Beckett: "I'm a medical doctor, not a bloody fighter pilot!" (Stargate Atlantis)
- Dr. Doppler: "Dang it, Jim, I'm an astronomer, not a doctor! I mean, I am a doctor, but I'm not that kind of doctor." (Treasure Planet)
- Will Smith: "Dammit, Jim, I'm a black boy from Philly, not a doctor!" (The Fresh Prince of Bel-Air)
- Zoolander's Father: "Damnit, Derek, I'm a coal miner, not a professional film or television actor." (Zoolander)
- McCoy: "Forget it. I'm a doctor, not a patsy." (Family Guy)
- William Shatner: "Dammit, I'm a Doctor, not a... oh!" (Saturday Night Live)
- Leotard Buns McCorduroy: "Dammit Gym, I'm a doctor not a... on my way sir!" Sev Trek currently available at Star Trek Minutiae
- Nita: "Sker', I'm a wizard, not an engineer!" (Wizards at War)
- On the TV series Unfabulous, Principal Brandywine uses lines that follow the pattern of, "This is school [or name of a school-related object or place], not a/an/the [event, time, place or object unrelated to school]!", or "You're a middle school student, not [a famous person who does what the student is doing]!", or "I'm a middle school principal, not a doctor [or other jobs outside school]!"
- An elderly man, when inquired about potions: "Dammit Jim, I'm a doctor, not a miracle worker. Ask someone else!" (Final Fantasy IX)
- Marvin (the manic depressive robot in the motion picture of Douglas Adams' The Hitchhiker's Guide to the Galaxy) after being told to "freeze", states: "I'm a robot, not a refrigerator."
- In the animated TV series X-Men: Evolution episode 7, "Storm", a mutant with weather altering powers,says "I'm a weather witch, not a snowplough!"
- Stranded with four others on a deserted planet in "a Donner party situation," McCoy says, "Dammit, Jim, I'm a doctor, not a–" then is interrupted by the others saying "–a cannibal, yes, we know, we know." McCoy then lowers his head and asks himself, "Am I really that predictable?" (Robot Chicken)
- At one point in the Wii video game Trauma Center: New Blood, surgeon Valerie Blaylock says "We're doctors, not diplomats!"
- In Spiderman 3, when asked about the mysterious black substance shown him, Peter Parker's science professor remarks, "What do you want me to do? I'm a physicist, not a biologist."
- On the television series Eleventh Hour episode 11 Dr. Jacob Hood, trapped with his handler in a freezer remarks, "I'm a scientist not MacGyver, shoot the door".
- Dr. McCoy (voiced by Frank Welker): "Darn it Yakko, I'm a doctor not a magician." (Animaniacs)
- Robot running soda fountain: "I am a robot, not a miracle worker." (SpongeBob SquarePants)
- Miss Tutweiller: "I am an educator, not a warden!" (The Suite Life on Deck)
- Dr. Valsh, in response to Phil Wenneck's request for directions: "I'm a doctor, not a tour guide." (The Hangover)
- Fred: "I'm not a resistance fighter, I'm a doctor." (V (The Final Battle)
- Taran: "I'm a warrior, not a pig keeper." (The Black Cauldron)
- Tailor "I'm a clothier, not a doctor." (Schlock Mercenary)
- Jean Valjean: "This is a factory, not a circus!"" (Les Misérables)
- Ambassador Dennis Crocker: "Damn it, I'm an ambassador, not a doctor!" (Fallout: New Vegas)
- In a sketch depicting every episode of Star Trek, by comedy group the Frantics, McCoy says, "I'm a Doctor, not a physician."