The second most notable is the body count. Hamstergeddon being a good example, with at least one school bus being eaten, and two people being stomped on but totally not killed,or so Nick says. The writers know better.
According to the very same wiki, 70 people die in Hamstergeddon.
The computer used to evaluate the students' tests in Career Day? The POS 2000.
For those of you who aren't acronym-savvy, POS means "piece of shit".
Also in the first episode, the call letters of the radio station that can be seen while Zim does the flyover of the planet? WTFU.
The Zim wiki claims it stands for "Wake The Fuck Up."
In "Battle of the Planets," the seat Dib's sitting on while piloting the butt on Mercury is in the very center of the butt.
'"Halloween Spectacular of Spooky Doom,"' just... Halloween Spectacular of Spooky Doom. If you've read Jhonen's previous work and you have not seen Invader Zim, or have seen Jhonen's previous work... lets just say it's what you'd expect of Jhonen if you had him write for a kids show and then make a halloween episode. Which is exactly what he did in, say, Johnny the Homicidal Maniac. (speaking of him, he appears amid a mob of monsters in the episode!) It is crammed full of nightmare fuel from start to finish, broken only by snatches of nightmarish, surreal humor or GIR, so much Nightmare Fuel that even Jhonen has said he has no idea how it got aired. They even managed to get blood past the radar-when Dib manages to crawl through the portal in his head, for a brief moment his body is inside out, he hits a fence, and you can clearly see blood on it. And, you know, his organs. Very realistically and Squick-inducing too.
Dirty Chicken. That is all.
In "A Room with a Moose:" "I'm about to punch you in your wormhole!"
Zim threatens to send Dib to a dimension of "PURE DOOKIE"!!! We don't actually see the screen, but it emits a light that turns Dib and the whole room brown.
Right at the beginning of "Dark Harvest,"
ZIM after getting hit with a dodgeball: OW! MY SQUEEDLYSPOOTCH!
Dib: Did you hear that? He said squeedlyspootch. That's not a human organ!
Gaz: I have a squeedlyspootch.
Speaking of "Dark Harvest," that whole episode must have been slipped in under the radar. Way too much Body Horror for Nickelodeon.
At one point, Dib is looking at a female classmate with his x-ray goggles and sees that something in her lower abdomen has been replaced with a cat.
The episode "Plague of Babies" has Zim walking in on GIR blowing into a power amplifier. Unfortunately, it looks more like he's smoking a bong.
Since this episode has a large plot point taking place in a maternity ward, there is always a risk of The Talk coming up. Zim, of course, Lampshades it.