Crocker's fantasy to become supreme ruler of the world was mentioned in Transparents! and becomes a reality in the 3rd act of this movie.
Crocker also wears similar armor that he wore in his fantasy, with the only major difference being that it's now blue instead of white.
More subtly, after turning some students into ice sculptures, Crocker mentions how he wanted to turn into piles of ash, which is what he did to Principal Waxelplax and another teacher in his fantasy too.
There was an unseen picture from the "The Switch Glitch," where Timmy was wearing a dress.
The Fairy-versary muffin would later make a cameo in "Wishology! The Big Beginning" where Timmy grabs one from a pile of regular muffins, but rejects it.
Most godchildren only have their godparents for less than a year before they're revealed and taken away.
Before Timmy and Crocker are transported to the subatomic world, it shows a cartoon version of Butch Hatman, the creator of the series, most likely working on an episode script or scene sketches, before zooming in on his pencil's eraser.
The music playing from Crocker's van disguised as an ice cream truck would later play in the ChalkZone episode "Let's Twister Again". Both shows were produced at Frederator Studios and were composed by Guy Moon. This is one of the few instances where background music from The Fairly OddParents would show up in ChalkZone.
Mr. Crocker blasting the nose off the sphinx he brought to life is a reference to The Great Sphinx of Giza that, for some reason, doesn't have a nose.
The title "Abra-Catastrophe!" is a pun of commonly used magic phrase "Abra-Cadabra".
Butch Hartman - Elmer Apeman is a pun off of the show's creator's real name.
A Knight's Tale - When Cosmo (who just received large muscles) was about to punch Crocker, he yells "Wandaaa!" in a similar manner that William Thatcher yells "Williaaam!" as he was about to strike his opponent.
Marvel Comics - Crocker's outfit seems to be a cross between characters Galactus (head and armor) and Annihilus (wings and staff).
Timmy's disguise, the white hood of his cloak hiding his face, is similar to Moon Knight.
Planet of the Apes - The world ruled by primates is a take on the movie. The Abraham Lincoln statue at the Lincoln Monument turning into an ape is specifically a reference to the 2001 remake of the movie.
Harry Connick Jr. - The song "Wish Comes True" was played by a character named Fairy Cowlick Jr.. The joke is made more obvious in the Latin America dub by naming him Magic Connick Jr..
Groucho Marx - Timmy's receives a Groucho Marx mask from the April Fool and his line he uses to trick Crocker: "One of America's most beloved comedy entertainers" references him.
Three Stooges - Crocker's line: "You're not Shemp! You're not even Curly Joe!". refers to characters in the later "Three Stooges" shorts. Shemp, and later Curly Joe were replacements for the then deceased Curly Howard as the third stooge in the late '40s and '50s.
Popeye the Sailor Man - The sailors crowding around Crocker's spinach van is a play on how Popeye eats spinach and suddenly obtains superhuman strength.
The world's famous landmarks changing from normal to abnormal and vice versa.
When Sanjay throws the magic muffin during the food fight, it's whole, even though the muffin man had previously taken a bite out of it.
When Mr. Turner filmed Timmy eating spinach in the flashback, the bowl was normal size. When it was shown on the TV, the bowl was the size of a small cup.
Also while he was being filmed, Timmy looked at the camera, then to the spinach, and then back to the camera. When Mr. Turner puts the tape in, however, Timmy just rolls his eyes.
This episode shows that Vicky had been babysitting Timmy for several years before he got his faires, yet in the pilot Timmy met both her and his godparents on the same day.
When 14 year old Vicky compiles Timmy's tapes into one, her lips briefly turn pink like they normally are before reverting back. Her pink lips also appear on the poster that Timmy called her from.
In similar vein to the goof above, the Fairy-versary Muffin emblem on Crocker's suit is inconsistent in the way it is drawn.
The DVD's closed captioning writes Chester's line as: "May I go to the Sand cave?" instead of "May I go to the Sanjay?" when he asks Mr. Crocker the question after Sanjay's head is turned into a toilet.
When Timmy and Crocker are in space, Timmy poofs his mask to a helmet, causing him to lose his disguise that masks his face from Crocker, yet Crocker somehow doesn't recognize that he's Timmy. Timmy also takes off his disguise entirely for the mid-battle tea party earlier, with Crocker still being oblivious to his true identity.
The cage that the apes trapped Timmy in strangely lacked a lock.
When Mrs. Turner wraps Mr. Turner's legs with an apron in the flashback, it changes to a rope when he is pulled back.
After Crocker turned the students into ice sculptures and toilets, those kids disappear for the remaining scenes in the classroom.
In the picture supposedly from the episode, Dream Goat!, Vicky was wearing a goat lover outfit and standing in front of a window while giving Timmy a wedgie. However, in both times she gave Timmy a wedgie in the actual episode, she wasn't near a window and didn't wear the outfit until the second wedgie.