One of the most notable and hideous examples is the image of "Bloody Gir," which Nick Toons refused to publish. In response to this, the image has been hidden within a single frame in several episodes. The easiest to spot being the one hidden in the intro of "Mortos Der Soul Stealer"
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.
5 people die in "Attack of the Saucer Morons," according to the Invader Zim wiki.
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.
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.
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.
In "Halloween Spectacular of Spooky Doom," 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 Gretchen 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.