An Arm and a Leg: The firefighter defeats Captain Crocktopus by slicing off his mechanical arms (and apparently, one of his real arms) with her fire axes.
Basement-Dweller: As previously established in the Crimson Chin's debut episode, his author, Elmer Marmelman, lives in the basement of his parents' home. He even subscribes to a monthly magazine called "Nerds Who Live with Their Mothers".
Captain Ersatz: It's easier to list the characters who aren't turned into one as a result of the titular wish. Notably, in amongst the more obvious parodies (The Baby Shredder, Captain Crocktopus, etc), there's also Matter-Muncher Lad, based on the relatively obscure Legion of Super-Heroes member Matter-Eater Lad.
The episode's plot is kicked off when Timmy wishes that everyone on Earth had superpowers. However, everyone means everyone, including Vicky, Francis, and Mr. Crocker, who are turned into supervillains.
When Timmy inevitably decides to unwish the wish, he words it terribly, allowing the Nega-Chin to explain this trope and twist the resulting wish.
Timmy: I wish for a world without superheroes or— [the Nega-Chin clamps his hand over Timmy's mouth before he can say "supervillains"] Nega-Chin: You heard him! He wished for a world without superheroes! You must grant it! [Cosmo and Wanda reluctantly raise their wands] Wanda:These loopholes are so annoying.
Four-Man Band: The Nega-Chin's group is a villainous example:
I Want Grandkids: As the Crimson Chin author is dragged out of his home by the Nega-Chin, his mother yells out "Don't come back unless you bring me grandchildren!".
The Real Heroes: Once Timmy accidentally wishes all superheroes out of existence, it's up to Dimmsdale's regular heroes (including a firefighter and a milkman) to defeat the villains and save the day.
Shout-Out: On top of all the various superhero and supervillain Expies, when Elmer's boil is popped by The Baby Shredder, he deadpans, "Curses! Boiled again!", riffing off the catchphrase of Doctor Sivana.
Take That!: Veronica's alter-ego, Hawkgal, is a rather unflattering parody of Hawkgirl. While Hawkgal's lameness is mainly to reinforce Veronica's own Butt-Monkey status, it can't be a coincidence that she's based on the Distaff Counterpart of one of DC's two biggest Memetic Losers.
Wolverine Wannabe: The comic book version of Vicky (or rather, The Baby Shredder, rather) is a villainous example.