- Hall passes at the Skool take the form of an Explosive Leash.
- A lot of the music from the series has titles that are humorous Shout Outs. The best was the theme in "Walk for Your Lives" when the slow-moving explosion is let out on the city, which was called Happy Fun Ball. Another one from the same episode has the theme for when Zim is studying the explosion, with the title Analyze This.
- The conversation between the Planet Jacker pilot and co-pilot was a Shout-Out to a similar conversation in Fargo. Plus threats of cephalophagy.
- Hamstergeddon is an inversion of Gamera, with the military unwilling to cause Peepi any harm at all and repeatedly brushing off Dib's pleas to terminate him with extreme prejudice. Ends with a subversion of Gamera's Deus ex Machina ending.
- The Megadoomer is a take-off on the EVA robots, the final battle in the Christmas Episode segues into a parody of End of Evangelion.
- Tak's plan to hollow out the earth is a send-up of the 1966 Doctor Who movie Daleks' Invasion Earth 2150 A.D.
- The "My vision is impaired!" GIR shouts out in GIR goes crazy and stuff is also a reference to the Daleks.
- The cutting edge video game in "Game Slave 2" is a clear homage to Vampire Hunter D.
- The Queen Louse in the episode Lice is a parody of the Alien Queen in the film Aliens.
- As is the scene in "Attack of the Saucer Morons" where Zim threatens to lay eggs in the human's stomach.
- GIR is dressed as a Xenomorph in the Halloween episode's opening.
- Zim's original plan to destroy Dib in Bad, Bad Rubber Piggy is an obvious reference to Terminator.
- Dib's final form in Bad Bad Rubber Piggy? A Mad Cat from Mechwarrior.
- You can see Max's head on one of Zim's walls.
- Zim's birth (read: decanting) echoes Brave New World.
- The "brainwashing" of the robot parents in "Parent Teacher Night" is a blatant reference to A Clockwork Orange.
- The black robots floating about the auditorium in "Voting of the Doomed" look eerily like the Death Star torture droid from Star Wars.
- Bolognius Maximus is one big shout-out to The Fly (1986), specifically the scene in the bathroom with the computer.
Dib: Computer, have I absorbed the bologna?Computer: No. Subject Dib has been fused with Subject Bologna.
- On the official Nickelodeon website, one of the Invader Zim games is titled "Good GIR Gone Bad".
- Zim's treatment of Nick seems like a more intentionally malicious version of Stimpy's Invention, although this could be coincidence.
- The chant "Bow Down Before the Power of Santa" from The Most Horrible X-Mas Ever is eerily similar to the Overture from Les MisÚrables.
- The high-pitched straining noise made as the portal in Dib's head closes in Halloween Spectacular of Spooky Doom is unsettlingly like the noise of the gate to hell closing in the climax of Hellraiser II.
- In his human disguise, Zim wears a wig and contact lenses that cover his eyes completely, just as David Bowie's character in The Man Who Fell to Earth does. Although, Bowie's Thomas Jerome Newton is able to conceal his identity because his disguise is actually good, rather than Zim's working due to the sheer stupidity of the human race.
- "I'll get you back! Maybe not today, maybe not tomorrow, but soon!"
- Issue #5 of the comic series goes into almost Reference Overdosed territory with its shout outs to various video games, starting with the title "The Humble Bundle of Horrors" and continuing with:
Shout Out / Invader Zim
"So, Jhonen, was that your oh-mahg to... ?"