Just about any fight scene happening in the series, for a short example.
As well as any of the intros depicting Jacknife, or rather, some of the things that Jailbot does to him in apprehending him.
The hallucination scene at the end of Don't Be A Negaton quickly turns downright disturbing, especially with the rotting dog and other horrifying trippy visuals. And then it appears that the demons actually became real.
D.L. Diamond's actual face without his wig or makeup is rather gross itself, when he's exposed as a sore-infested and decaying fraud (leading Jared to recognize him).
Mr. Grumpy-Pants: The Warden giving birth to a grotesque demonic-like spawn version of himself born out of his own bitterness, complete with dangling umbilical cord and all, and, later in the episode, him going back inside of him. To add to the grossness? It then gets vomited out through his mouth, shrieking a chilling "HAPPY BIRTHDAY, BITCH!" at its intended victim ("Sanser").
Cancer's death: The inmates throw her a huge party when they mistake her estimated death date as her birthday. They manage to pilfer Warden's own birthday items in order to do this. However, unbeknownst to them, "Sanser"'s health gradually worsens as she coughs up blood from organ failure. Her luck gets worse as she winds up slowly dying over the course of her "birthday", gets nearly strangled to death by the Warden's Inner Child, and in the coup de grace, is crushed by a huge pile of falling gift boxes.
Jailbot's dream of being the Warden's human(oid) son in "Dream Machine" may be one of the scariest non-violent parts of the whole show due to the Uncanny Valley animation (of the CGI David Wain as the Warden, and Jailbot being a little boy that still bears the dot-matrix face).
There's also a part where the Warden dreams of his crotch morphing into Jared's head and face, while his dream version of Alice quickly rots into an angered zombie ("I need my BEAUTY SLEEP!").
Its even worse once the Time Police judge shows the evidence, which depict the entire world going against Superjail and getting defeated easily by them and the Warden directly being involved on the battlefield; the surviving nations' leaders launching WMDs across the world as a last resort to defeat Superjail; the leaders trying to sign a truce to end the war, only for the person signing it to get pissed and try to stab him, resulting in all of the leaders getting killed by a laser, with the Warden saying "Guilty has charged" and then laughing about it; and The Warden then enslaving the planet.
Then there's the mind screw ending to Time Police part 2: After the Warden and his temporal duplicate cause a massive time paradox to happen, the judge of the Time Court is destroyed, causing the timeline to be wiped out. In the new reality, Superjail is reduced to an apocalyptic desert, and the Warden is shown as a crying newborn...who is then breastfed by Alice (who has become an elderly woman). And then reality is reset once more.
The original climax to Hot Chick had some disturbing overtones before the whole sequence was rewritten and redone throughout production of the episode: The now-helpless and horrified Hunter is piled upon by a bunch of sex-crazed inmates, who all at once instantly start attempting to rape her (or going through with it). The Warden himself becomes horrified that the inmates are defiling the woman he's had a crush for, only to then laugh things off after he sees that she's morphed back into her goo form, out of her desperation to escape the inmates' brutality ("Is there anything she CAN'T do?"). Then just as in the finalized episode, there's a revelation in the sequence afterwards that Hunter is apparently an alien dog. Meaning that the inmates not only assaulted a woman, but basically committed bestiality.
The ending of The Budding of the Warbuxx, which the Twins (having been revealed to be aliens since "Hot Chick") eat the "Warbuxx bud" that one of them had just given birth to, complete with their tongues splitting into insect-like pincers when they devour it.
Even worse, the Warbuxx doesn't bleed when they eat it, but in the final scene after Alice sends its decapitated head to a starving child? The child takes a good bite into the head, causing red blood to spray out. If that weren't enough, the Warbuxx's head then makes an agonized face in response to being bit.
Ash was trapped in a burning movie theater as a child, waiting and waiting for his drunken father to return (said father was responsible for the fire due to a lit cigarette). It's inferred that this is how he was severely disfigured, but rather than fear the fire, he began fearing movies due to the negligent father leaving him all alone.
If the scene of one Twin's belly ripping right off in the budding disturbed some, the original idea in the storyboards (even if not directly shown) was a bit more gross in the implication: The Warbuxx came out of his ass.
Some of the visuals in the sex sequence in Stingstress are quite disturbing, for a matter of understatement. The sequence is filled with flashing and shifting colors against constant visual metaphors for sexual acts (one of which — Alice having an actual jackhammer for a penis pounding away at the Mistress's literally-depicted clam — had to be blurred out as it went too far for Cartoon Network), with the scenery and characters morphing in an homage to Malice In Wonderland (which is rather Nightmare Fuel-worthy in itself). To top it off, we're treated to shots of Gary and Bird's eyes exploding and melting out of their skulls (Bird's even turning into eggs), as well as the same happening to Lord Stingray.
Superfail shows brief shots of some horrific childhood flashbacks, each time as Warden hits his head in his fall. These include being violently spanked by his father, and a creepy inmate grabbing the child Warden (and who knows what he intended to do?). Of course, the main flashback sequence through the episode involves a memory of the young Warden meeting an unwanted guard puppy... and it all goes downhill from there to showing just how sick and twisted his father really was.
There was also a creepy gag that went too far for the Williams Street censors, within the flashbacks to the Prison Mogul's jail: A bunch of vicious dobermans are shown gnawing and cannibalizing each other, and an unlucky inmate winds up disemboweled and torn apart by the hungry dogs. The man having his organs spill out was deemed to be too violent, so a large black censor bar (with a red "CENSORED" caption) suddenly covers the scene as the dogs tear at him. The uncensored version was once available on the layout artist's Deviant ART, but the network's legal team ordered it taken down (and truthfully, it's one instance where this troper would actually have to side with the network as the scene censored alone was creepy... but seeing it uncensored would be borderline grotesque.)
The Trouble with Triples ending: So the Twins appear to win their brood war after all (on a technicality due to their father deciding NOT to disqualify them, because he was impressed by them "including" him in the fight via the Warden stabbing him), but instead of getting to remain at Superjail, their father decides he'll be taking them home to be overlords and "study". The studying includes him flooding his sons' minds with horrific images and sounds, with their eyes forcibly pried open (ala Clockwork Orange) to have lasers fired into them, fluid forced through their mouths and noses, and wires tearing through their ears and noses to the point of them bleeding. This is all shown in several unsettling closeups, with the Twins' complaints rapidly increasing from "boring" to wanting to die.
Burn Stoolie Burn has the entire jail go down in flames to Warden's newfound love of fire, with Jailbot seemingly being destroyed in an attempt to save Alice and Jared, and then Jared himself (after having previously been burnt by Warden) being shoved back into the flames by Lord Stingray and Alice unknowingly abandoning him until she realizes that Stingray was the one who boarded the escape pod with her.
Then there are the Superhell demons released up into the jail grounds, who violently slaughter and torture those they come into contact with. And while the jail's burning, they're free to run wild and kill anyone else who hasn't burned to death. One HELL of a cliffhanger, indeed.
In "Jean, Paul, Beefy and Alice", the Twins take advantage of Jailbot's need for love by having him fall for some grotesque..thing...that ends up infecting everyone in Superjail and causing a terrifying case of Body Horror to befall both the inmates and the staff. The Doctor surmises that killing the creature Jailbot has feelings for will return everything to normal, but it turns out that he is incorrect. And then the episode ends.
Superstorm! has the Doctor apparently wanting to date rape Sharice, not to speak of all the grotesque furniture and things made up of human (and inhuman) bodies in his lab.