These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Sometimes Zorak and Moltar remind us all too well that they're dangerous criminals; Moltar mangled and ate Meatwad in "Baffler Meal" but treated it like a totally normal practical joke, and Zorak is so cruel he can eat his own nephew free of remorse.
Although Moltar only killed Meatwad because Meatwad begged him to.
"Funny Aneurysm" Moment: In the episode where Susan Olsen was being interviewed (circa 1996), Space Ghost's evil twin Chad asks her if shes related to Mary-Kate and Ashley Olsen. He then goes on about how freaky-looking they both are. In 2004, Mary Kate entered rehab for anorexia.
Ho Yay: Bobcat Goldthwait asking Space Ghost if he's pretty and this scene from the episode "Live at the Fillmore".
Space Ghost: Moltar, reach down my pants and get the show budget to pay the bail. Moltar: No! Zorak: You know you want to. Moltar: ...I know.
There was probably enough of this to warrent its own page on the Ho Yay trope (or at least combined with the other Williams Street cartoons).
Jump the Shark: Once the show made the move to [adult swim], it focused less and less on the interviews, and more on gore, Nausea Fuel, and Surreal Humor. By the time the show ended, the only thing it had in common with the original was that it featured Space Ghost, Zorak and Moltar.
When I was little I couldn't watch the episode "Curses" without having nightmares of a red-eyed Space Ghost coming to eat me. Even today the episode is a bit hard to watch.
Recycled Script: "Kentucky Nightmare" and "Baffler Meal" are virtually identical in concept (Space Ghost sells out to a fast food company, which injects obnoxious advertising into the show, and Willie Nelson is the guest). However, it's justified in that "Kentucky Nightmare" was intended to replace "Baffler Meal", which the creators never intended to air (but several years later did).
Seinfeld Is Unfunny: This show was unlike anything else on the air in 1994 and only got more "out there" as the series progressed. Now almost the entire Adult Swim lineup has taken some cues from this show and it's more difficult to see what made it so special.