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.
Zim wearing tissue boxes on his feet in the episode "Germs"
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.