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.
Jan and Wayne's marriage slowly falls apart as the series goes along due to Jan's implied affair with Steve Brule.
Steve himself is an extremely awkward manchild.
Casey is obviously a parody of severely mentally challenged kids who have amazing talents.
Tim and Eric themselves. Tim is starved for attention and even his own parents favor Eric over him, and Tim pushes Eric down the stairs in the 50 anniversary reunion episode. By the Chrimbus Special, it's apparent that Tim's hate for his partner and self-esteem issues are festering and festering hard.
Ear Worm: "This is what I do, I sit on you, sit on you, sit on you!"
"Funny Aneurysm" Moment: As Tim and Eric are explaining their decision to "Fire [their] friends, and hire old men" in "Abstinence", Tim mentions "an old man working here named Richard Dunn, who has passed away." However, Tim goes on to say "He taught me many lessons about learning about life," (almost) turning this into a Crowning Momentof Heartwarming..
From the very same episode: in the "Lazy Horse Matresses & Bedding" segment, the address of the store is "Exit #37 off the Richard Dunn Memorial Highway". Granted, Dunn was an old man by that time, but it's still kind of eerie.
Second cake taker? The Chrimbus special, during the Chrimbus Carol sketches. Carol gets angry at Mister Henderson while his head is under a guillotine blade. Instead of taking his head off in a comical fashion, the blade cuts halfway through his neck and he lies there in agony, thrashing and coughing up blood. Absolutely horrifying by how realistic it was.
Word Of God (from Tim) says that the show is supposed to be "the nightmare version of television," so perhaps the prevalence of Nightmare Fuel ought to be expected.