Ms. Crabtree's character design and abrasive personality sometimes crossed into this territory for the first three seasons, to the point it even, in-universe, scared the living bejesus out of characters like Mr. Garrison, Chef, and even Cartman!
Cartman is generally frightening when he gets some of his Ax-Crazy moments.
Like the time he ground up a kid's parents into chili and tricked the kid into eating them. And, to top it off, sang "Nyah, nyah, nyah, nyah, nyah! I made you eat your parents!"
"Do you like it? Do you like it, Scott? I call it: Mr. and Mrs. Tennorman chili." The look on his face seals the deal.
"Let me taste your tears Scott. Mmmm, your tears are so yummy and sweet!"
Stan and Kyle put it best...
Kyle: Dude, I think it might be best for us to never piss off Cartman again.
Stan: Good call.
This is more of a Fridge Horror, but certainly qualifies. While Cartman almost always proves somewhat immoral and sociopathic behavior, is somewhat frightening if you think how he will be when he grows up and becomes an adult. If he has made one of the most sadistic and cruel acts in a TV series ever done (but played for laughs), as shown in "Scott Tenorman Must Die", imagine how inhumane he could be as an adult.
The most chilling thing in Cartman is how desensitized is this kid to killing, when he planned genocide and murder during previous seasons (the "Coon & Friends" trilogy is an example), before his redemption in "Jewpacabra". Not only surprised his coldness to not forgive anyone, if not also his twisted mentality, just look at The Woodland Critters he created. It really is a kind of fear even to his own friends.
The show's unsettling fixation on suicide. It really makes you wonder about the mental health of the creators.
In the episode "Marjorine", the reaction of Butters' parents when they think he's committed suicide, especially his mother's shriek when she sees his "body" hit the ground. It is one of the few times that I've found the show to fully cross over into Dude, Not Funny! territory.
The multiple gay suicides at the camp Butters is sent to in "Cartman Sucks" might've been darkly funny when the episode first aired in 2007, but the recent rash of real lifegay suicides and homophobic hate crimes between 2010 and 2011 really give the episode a darker feel.
Kenny McCormick's deaths. Sure, it is played as a runninggag, but there are quite a few of them not for the faint of heart.
"Mysterion Rises" makes it even worse combining Nightmare Fuel with Fridge Horror, Kenny states that he is unable to die:
Kenny: I can't die. I've experienced death countless times. Sometimes, I see a bright light. Sometimes, I see Heaven or Hell. But eventually, no matter what, I wake up in my bed wearing my same old clothes. The worst part? No one even remembers me dying. I go to school the next day and everyone is just like "Oh, hey Kenny," even if they had seen me get decapitated with their own eyes.
Also, when Cartman once badmouthed her behind her back, he reacted with absolute fear when she addressed him. Oh, and not to mention she's based on Trey Parker's sister (though the worst she did to Trey was push him down some stairs, lock him out of the house, and punch him in the face. Compared to what Shelley does to Stan on the show, it's nothing).
The Woodland Christmas Critters?
Jason: Man, I do not want to meet the kid that dreamt those things up. [jump cuts to Eric Cartman]
Kenny's death. It even has a small Hope Spot before coming to a bloody end.
Kenny getting sent to Hell, complete with demons fighting over him.
Don't forget that, according to the movie, almost EVERYBODY goes to hell. Kenny even runs into Gandhi down there!
The M.A.C. in general. It starts out as another of Sheila's Moral Guardian soapboxes, but it quickly escalates into a plan of war, mass murder and genocide. All because of a dirty movie.
The war itself, with soldiers on both sides getting shot, stabbed, beheaded and dismembered.
"Cartman Gets an Anal Probe" where the "dream" that Cartman insists he had about aliens probing him doubles as an in-universe example.
The Grim Reaper chasing the boys in "Death."
Grampa Marsh's grandfather. Enough said.
The end of "Pinkeye," when all the zombies revert back to their normal selves and we see a TON of dead bodies scattered around the field.
Very narrowly averted with "Starvin' Marvin." The episode was originally going to end with Sally Struthers being killed and the Ethiopians feasting on the fat from her belly for Thanksgiving. However, Comedy Central would not allow the episode to end in such a way. So it ended with Struthers being tied up as the Ethiopians feasted on Dr. Mephesto's cloned turkeys.
Stans's hellish vision of Kyle's parents in "Ike's Wee Wee".
"Let us cut off your wee-wee, Stan!"
Seeing the remains of the people everybody was forced to kill and eat in "Cartman's Mom Is Still A Dirty Slut" could definitely give some kids nightmares.
Another early example can be seen in "City on the Edge of Forever", in which the children are trapped on a school bus teetering off the edge of a cliff. One of the students, an actual Red Shirt, decided to take his chances outside even after Mrs. Crabtree said there was a big, black, monster outside. He seems alright at first but then the monster attacks, grabbing him and pulling him into a tree. As the students watch on to learn of his fate, WHAM! His eviscerated body hits the window. The children think they're safe until the monster rips the top off the bus and steals Kenny. Yes, it was All Just a Dream from Stan but the fact remains. That monster was something that comes from the bowels of your worst nightmares◊.
Seeing the remains of Tom and Mary at the end of "Cow Days." Granted, they were just extras with little significance to the episode's plot. But still...
"Trapper Keeper." On one hand, it's an awesome episode with a cool homage to AKIRA (among other sci-fi classics). On the other hand, it has an homage to Akira. And then the B-plot is about Rosie O'Donnell...
In "Hellen Keller", Cartman's blindfolded and has headphones put over his ears in an attempt to understand how it'd feel to be Hellen Keller to get inspiration for lyrics, every time he closes his eyes, he sees horrible stuff, like a body being opened up, a rotting corpse, war, an atomic bomb going off, a rat eating a dead rat, a man on fire, a mime and other stuff. Cartman mentions that he sees that everytime he closes his eyes. What makes this scene even worse is the fact that all the aforementioned footage is shown in live-action.
In "Fat Camp", the manatee dissection scene. They use actual photographs of various muscular structures. Then the ridiculous amount of peer pressure Kenny receives regarding the manatee spleen. First Stan and Kyle make him dissect, then the other kids get him $41 to eat manatee spleen, then an additional $19 to eat the regurgitated spleen. This leads to Kenny's rise to fame as a gross out stuntman. The whole thing is really frightening because it all started with his friends egging him on.
People vomiting up their intestines in "It Hits the Fan".
The ending of "Ass-Pen" is also a little... troubling, to say the least. To wit, the scene where the nerdy girl lifts up her shirt to reveal two grotesque creatures in place of her breasts.
In "Freak Strike", when the freaks tell Butters about the time they killed a freak impostor ("Lobster-boy", who actually was just a normal lobster) by boiling him alive, and we see Butter's imagination of the lobster cooking in a scalding metal cauldron, complete with eerie piano music and the sound of the lobster crying in slow agony.
Wendy getting breast implants in "Bebe's Boobs Destroy Society." There's tons of blood and it's uncensored! (in the Comedy Central version at least; a lot of network TV syndicated versions will not air this scene due to gore, nudity, and the doctor's constant cursing).
"The Death Camp Of Tolerance".
How Christopher Reeve uses stemcells.
In "'Lil Crime Stoppers", the boys continually want to solve crimes in South Park. Despite the simplistic nature of the incidents (stolen pie, lost doll) they essentially screw Occam's Razor and come up with insanely brutal motives. Some of the details include having a older gentleman beat his wife with a hammer, decapitate her and dissolve her body in acid. Another has a pedophile looking into a girl's room and cutting himself in pleasure.
How 'bout poor Butters getting a ninja star in the freakin' eye. And his anguished screams afterward, and how they have to cover it up... Talk about the designated Woobie.
Passion of the Jew. Kyle has an EXTREMELY DETAILED dream where Jesus is crucified, and Kyle, in the end, is the one poking Christ with the spear. *shudder*
The scene in "You Got F'd in the A" where a traumatized Butters is looking through the box containing his old tap-shoes. The music starts off sad and sentimental as he looks through the articles about his winning performances, then turns darker and creepier, as do the articles. Later, we get a flashback to the trauma: during his last performance, his tap shoe flew off and knocked down one of the stage lights, setting off a small-scale massacre as people were cut in half by wires, crushed by falling objects and trampling one another. Oh, and Butters gets splattered with their blood as he watches in horror. Only South Park could turn a tap-dance competition into that. And when Stan and some other kids finally convince Butters to tap dance again as part of a dance squad competing against a rival squad, he ends his performance by having his shoe fly off again, disconnecting some stage lighting and killing the opposing squad. Which makes the South Park squad the winners by default. Which results in Butters yelling out in horror as his inadvertent killing of six people is celebrated.
The episode "The Jeffersons" (The episode about Michael Jackson). The whole episode has a creepy atmosphere, but the worst part has to be the end of the episode when parts of the face of Mister Jefferson fell off, starting for the nose.
Then we have Trent Boyett, who was wrongly imprisoned because he was believed to be responsible for Miss Claridge's fate (in reality, the four main characters talked him into it). In his crazy drive for revenge, he hospitalizes Butters and a whole gang of older boys with a series of stereotypical bully attack moves (wedgies, Indian burns, noogies, etc.), but also a lot of nastier ones, like one which involves "tabasco sauce, a telephone, and the anus."
The boys' complete apathy when it comes to the situation, both Miss Claridge's fate and Trent's wrongful imprisonment. They do try to tell Miss Claridge that they caused the accident, but only because Stan's older sister made them do it in exchange for protection from Trent.
Mr. Garrison's Fancy New Vagina. All of it, including the opening scene, Gerald as a dolphin, and Kyle breaking his legs in his tall black kid body. Said opening is about Mr. Garrison getting a sex change, cutting between Mr. Garrison with live-action footage of a real sex-change operation!
In Ginger Kids, when the ginger kids swarmed and kidnapped all the non ginger kids, it was pretty horrific. That and Cartman came really close to succeeding in his plan to wipe out all non-gingers.
"The Return of Chef": He was burned, battered, impaled, shot, his face (including one eyeball) was pulled off, and his limbs were torn apart by a grizzly bear and a mountain lion, and he finally defecated as he died.
Kyle's nightmare in "Cartoon Wars" in which the town is attacked by terrorists, and Ike goes missing. Kyle finds him just as a nuclear warhead goes off, complete with a very graphic depiction of IKE'S BODY MELTING WHILE SCREAMING.
The ending where we see Liane spoiling Cartman and it zooms up to his face while "Ave Satani" plays.
The climax of Stanley's Cup. When the pee-wee hockey team that Stan is coaching go on to play against the Detroit Red Wings, they are brutally, horrifically, and bloodily beaten up. What makes this scene even more horrible to watch is the fact that Nelson, a kid on their team who came down with cancer, had to see this as the last thing he saw before he died. Doubles as both Nightmare Fuel andTear Jerker
Almost all the lice getting wiped out in "Lice Capades."
In "Night of the Living Homeless", a parody of the Zombie Apocalypse where the large group of homeless that overruns the town are the "zombies". Anyway, this episode is one part Wall Banger, one part Nightmare Fuel. And both are in the same few minutes. When the kids traveled to Evergreen, Colorado, the last place these "zombies" were, there's only 3 guys left in the entire town, carrying shotguns and wearing filthy, plant-covered clothing. They tell the kids of how the homeless flooded their town, moaning about "change" (as opposed to brains). Eventually though, the homeless got enough to rent apartments... soon, it was impossible to tell who was "homeless" and who was not. The Wall Banger, of course, was that if you could rent an apartment, you weren't homeless anymore. But everyone treated it like it was an actual, incurable affliction, like most zombies are. So, the "leader" of the three guys "found out" that his wife was "homeless". He was shocked at that "information" and wondered how could he have possibly missed this after 20 years of marriage! So, he had to kill her...with a flamethrower. The Nightmare Fuel comes in when the rubble behind the "survivors" starts shaking... and this gray, vaguely-human shaped thing rises from the rubble, moaning. That's his wife, still somehow alive despite having maybe about 75% of her flesh burned away. After some rather useless dialogue "You nurned ny ips ough! (You burned my lips off), she shoots all three dead, after sustaining several bullet wounds herself.
In that same episode, a scientist tries to shoot himself to death...and fails. He then proceeds to keep shooting himself all over his body, with many shots to the head and heart and still doesn't die. When he finally does, there's a huge puddle of blood underneath him. Just think about living in all of that pain. It makes you shudder, doesn't it?
The entire episode devoted to Britney Spears doing a graphically-animated impression of Mike the Headless Chicken. Urgh. (By the way, for more Nightmare Fuel, click that outgoing link.) Very little humor, lots of gore, and lots of biting, truly unsettling social commentary. For those too afraid to watch the episode, Britney shoots herself in the face after being tricked into thinking the South Park kids are her sons, but fails to kill herself and is left instead without most of the top of her head. She appears to be unaware of anything that's going on, but is still paraded around on stage as-is to do a concert. Being as in her current state all she's capable of doing is making a horrible gurgling sound she proceeds to get shot down by fans and media, and a frighteningly literal comparison is drawn between human sacrifice and the way society sets up celebrities, then viciously tears them down. The entire episode is both nausea fuel and nightmare fuel, but as always, Some Anvils Need to Be Dropped.
The scenes in "The China Probrem" with George Lucas and Steven Spielberg raping Indiana Jones. Those scenes were supposed to be played for laughs, but are nothing short of disturbing.
Doubles as Nausea Fuel: The idea of drowning in urine in "Pee."
In the episode, Insheeption, Stan, a sheep hearder and Mackey go into Mackey's therapy dream to reveal a field trip where Mackey runs from bullies, hides in a building and is molested by Woodsy Owl only to reveal Freddy Kreuger piercing Woodsy Owl's chest open and Mackey waking up so Stan doesn't want his therapy and Kyle asks how he knows that wasn't his.
In the episode "City Sushi" Dr. Janus and his multiple personalities were quite scary. Mainly the part parodying Paranormal Activity where he comes into Butters' bedroom, stares at him for 3 hours, urinates on his face, then beats him and leaves before he wakes up.
All the "shit" imagery in "You're Getting Old". Also counts as seriousNausea Fuel.
The end scene of 1% with Polly Prissy Pants. Cartman is more fucked up than anyone thought.
"Let Go, Let Gov". Where the NSA gets all their information from: hooking up Santa Claus to a machine.
The Black Friday shoppers brutally killing each other in "Titties and Dragons". What makes it worse that those scenes are mixed in with actual Black Friday footage to make you realize what's happening in the cartoon is no different from real life.
Towards the finale, when the kids go to the local gamestop to buy a console they have to go through a mile of BLOOD to go there. dozens and dozens of people were slaughtered because of human greed.