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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.
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.