As an iconic Nineties blockbuster with many quickly recognized quotes and scenes, this bit of pop culture gets brought up frequently in other works.
- Wonder Woman (1987): Cassie's best friend Georgia complains when she's asked to try to hack into an Apokoliptian Supercomputer with her Mac laptop, saying that despite it working in Independence Day that's not how things work. To her annoyance it works anyway, since the motherboard starts converting her laptop as soon as she finds a way to connect them.
- Captain Marvel (2019) gives the film multiple nods including Carol walking through the desert and dragging an alien behind her, similar to Will Smith's character doing the same here. This makes sense given that the film is set in The '90s.
- Pacific Rim: The Rousing Speech given to the drift pilots takes some very obvious and unabashed cues from the speech the president gives the pilots before the final battle in Independence Day.
- Tangled has Flynn quoting Will Smith's character with:Oh, mama, I have got to get me one of these!
- Doctor Who: In "Victory of the Daleks" a lone human aircraft takes on a huge saucer-shaped alien flagship.
- VH1's I Love the '90s devoted a segment to this film in the 1996 episode.
- The Late Late Show with James Corden has referenced this twice during Jeff Goldblum guest appearances.
- In the music video parody "thank u, jeff", James notes in the first verse "Then he won independence/From an alien mess" as he anxiously watches the movie on a laptop (specifically the scene where David's explaining the plan to take down the mothership). One of the backup dancers is dressed as David as well (the others are dressed as Seth Brundle, Dr. Ian Malcolm, and the Grandmaster).
- Goldblum finishes his "Drop the Mic" rap battle with Corden with "Hey, I just killed an alien/Hey, that's an Independence Day!"
- The Late Show with David Letterman had a ball with this movie and its surrounding hype in the summer of 1996.
- In the week or so leading up to its release, a Running Gag was showing part of the trailer but then cut in a clip of Dave having some kind of domestic dilemma: cold pancakes, a lawnmower that wouldn't start, etc. The aliens' death ray proved sufficient to fix said problem every time, and Dave cheerfully called up to them "Thank you space monkeys!"
- After the film opened, Letterman said the REAL reason everyone was seeing it was one particular moment...and ran the actual clip of President Whitmore's daughter telling her mom over the phone "Daddy let me watch Letterman."
- Finally, one Top Ten List was "Top Ten Signs You've Seen Independence Day Too Many Times".
- Saturday Night Live had "President Bill Clinton" (Darrell Hammond) review the movie in a Weekend Update segment. By far his favorite thing about the movie was the First Lady getting killed off, although he would have liked to see Whitmore be introduced to some strippers by Jasmine with that in mind.
- Duke Nukem 3D: The secret level "Area 51" in the Plutonium Pak expansion has several shout-outs. The Casse family's RV is seen near the start of the level, the salvaged alien fighter is found in one of the rooms inside, and the nuke control room has a screen showing a ship blowing up a Duke Burger restaurant in a parody of the White House scene.
- Fate/Grand Order: The rerun of Gilfes is taken over by "Space Ishtar" who is in a suspiciously familiar UFO.
- Final Fantasy XIV: The FATE Titles are mostly all Shout Outs, one of which is "Independence Ray".
- Metal Slug 2/X: The final boss is a Martian mothership with a very similar design to the one seen in the film. After the players defeat it, it tries to fire it's Wave-Motion Gun one last time, only for a Rebel Army plane to fly into its core forcing its final retreat.
- Star Fox 64 has Katina, which is the climax scene from Independence Day, complete with Bill Gray, a nod to Gen. William Grey, Robert Loggia's character in the movie.
- Terraria: The description for the buff granted by piloting an UFO says "It's a good thing you had a Mac", referencing the infamous bit of Plug 'n' Play Technology in Independence Day.
- The Angry Video Game Nerd has reviewed the Licensed Game based on the movie for the PS1 by Radical Entertainment and Fox Interactive.
- How It Should Have Ended: In a bit for the Pacific Rim episode Russell Casse from Independence Day appears before the Precursors, saying his famous line "Hello, boys! I'm baaaack!" before Gipsy Danger explodes.
- A video by Lindsay Ellis compares this film with the next big movie about an alien invasion, War of the Worlds, which came after the Real Life 9/11 attacks, examining how each movie portrays the aftermath of the initial invasion and how it affects society at large and individual characters, and how each portrayal was colored by the state of the real world at the time.
- The Nostalgia Critic tore into this movie in one episode, and launched a Running Gag ("BOOMER WILL LIVE") for several subsequent episodes in the process. A 2020 episode poked fun at the unsuccessful sequel.
- RiffTrax has tackled this film.
- In the South Park episode "Cancelled", a satellite technician tries to help Chef and the kids with the threat posed by aliens who have been using humanity as the unknowing grist for an intergalactic reality show. He's clearly modeled after David Levinson, and his Bat Deduction skills are a parody of this movie's third act hinging on David's Eureka Moment.