Superjail! has had many examples of scrapped ideas in its development over time. The whole series itself was originally pitched as a silent cartoon. Though the executives shot down that concept, Karacas and Warbrick convinced them to at least let the Jacknife openings remain without dialogue.
- The little girl in the pilot (who later became known as "Cancer") was initially planned to be Jacknife's daughter.
- The Twins were originally intended to be straight-up antagonists to the Warden and were going to be "super-criminals" that he imprisoned (and that were unable to leave). This concept was dropped, as the staff felt the Twins worked better if they were just strange troublemakers and not deliberately evil. The idea of them being rivals to the Warden in any sort of way was dropped by season 2, as Christy Karacas admitted that Lord Stingray basically replaced them in that role.
- An early Adult Swim bump advertising the pilot showed a few different designs than what appeared in the final product
. While the Twins didn't really change at all, and while the rest of the staff only had some minor tweaks to their color schemes, the Warden was vastly different and was far from the "sadistic Willy Wonka" image they settled on. Gary's facial features and hairstyle were also slightly different, and the jailyard originally had things like pyramids and a merry-go-round in it. The eyeball-shaped aircraft was also to originally be much smaller and have an open top, which Warden and the staff would pilot it from. - "The Budding of the Warbuxx" was originally to be more centered around Alice, and involved her believing that she started her period after she sat on a packet of ketchup.
- A deleted opening for the episode involved Jacknife being caught stealing babies, upon which he'd be beaten up and taken away by Jailbot. It only made it as far as the storyboard stage, while the usual "trip to Superjail" sequence never got off the ground. The animatic reel shown on the season 2 DVD uses recycled footage from the "Mr.Grumpy-Pants" opening as a placeholder for the rest of the lost sequence. However, the "stealing babies" idea did get recycled for "Oedipus Mess", but with the action taken much further than what they'd planned for "Warbuxx".
- The second Twin originally didn't have his belly fall off to bud the Warbuxx, but it was instead implied to come from... somewhere below, with there being a jump cut from him screaming to Alice pulling out said Warbuxx from between his legs.
- DVD commentary tracks for season 2 revealed that "Lord Stingray Crash Party" was originally much longer and had a bit explaining why Alice became angered at the Stars N Stripes' deaths ( She had sex with all of them before they'd got back to the jail), as well as two ideas the writers threw around that hadn't panned out: An episode involving Alice becoming more attractive (only to get rejected for still having a penis), and an episode done from the vegetable garden's point of view.
- "Time-Police part 1" had a sequence that was cut after the animatic reel, in which Jared would fantasize about usurping the Warden's job due to his sudden disappearance.
- "Time-Police part 2" originally ran nearly 15 minutes, and had to be significantly cut down. Scenes that were dropped included Warden lamenting his father's death (but only because he kicked over his blocks), an explanation of how the Twins got to New York, and Jared being fired from another dead-end job. Other scenes got swapped around in chronology, and some only had dialogue cuts made for time. The animatic reel of this version can be seen on the season 1 DVD extras.
- "Hot Chick"'s ending had to be revised in production: Originally after Hunter was separated from her crystal, the inmates were to pile on her and assault her with the intent of raping her. The Warden would express horror at the sight, until he'd then see that Hunter reverted to her goo form and remark "Is there anything she CAN'T do?". Alice was to also take away the crystal before this sequence. In the final product, Hunter would wind up sealed into her crystal by the Twins, and it would then be confiscated by Alice. It seems that the revised ending also came about to explain how the Twins got out of the crystal and how Hunter was trapped inside, as the final two scenes afterward remained the same. A remnant of the original sequence made it into the episode, with Hunter on the ground and looking terrified, although the context was changed to have her fear the Twins instead of the inmates.
- Hunter was to also have detail to her nudity, but the censors wouldn't allow for it. In the TV airing of the episode, a censor box was even placed over her breasts in one scene, despite the lack of nipples. It may have been for the sake of a gag, or as with "Gay Wedding", the shot may have still looked too suggestive for the network.
- The Twins' father was originally going to be more humanoid, bald, and resemble Leigh Bowery in overall appearance and costume. Though his look was changed for the actual animation (as Karacas wound up not liking the idea of the character showing too much emotion), the creators still reference him being based off of Bowery in the commentary track for the episode.
- Combaticus was originally meant to be a parody of the lead character from Powder, and would be mistreated by others at the jail for appearing weak and puny. In the final product, he never interacted in the jail and was only made for Fight City.
- "The Trouble with Triples" was briefly considered to be the finale for season 3, but that idea got no further than a bit of wondering. "Burn Stoolie Burn" was actually one of the earliest scripts written and sat on the backburner during production, until they decided to tweak it to fit as the season finale and added on the cliffhanger twist.
- "Ghosts" evolved from a plot draft that Stephen Warbrick considered, in which Cancer returns as a ghost. The idea was revised into a full-on ghost invasion/supernatural story, though Cancer did still appear in a cameo (and was snuck into an earlier background gag with Ash in "Mayhem Donor").
- "Rubber Bullets" by 10cc, which was used as the theme song of the pilot, was originally supposed to be the theme song of the entire series as well, but was replaced by Cheeseburger's "Comin' Home" when it was discovered that paying for continued use of the song would be too expensive.
