When watching Agent Xero's introduction, A.J. remarks how Timmy wishes to be like Agent Xero one day, and Timmy says that he's planning to do that in the future, foreshadowing the events of "The Modiwishers".
Ivan calls Chester a wimp in response to his fear of girls, a reference to the running gag of the canon episode "Fairy Friends & Neighbors!", where Timmy is called a wimp throughout the episode.
Neptunia says that Agent Xero/Lacey Shadows sounds like her, a reference to Mae Whitman, who voices both Neptunia & Agent Xero.
Nickelodeon/Cartoon Network/Disney - Before everyone starts watching the episode, Ivan mentions how the failed pilot episode of the Modifyers was shown to Nickelodeon (referenced as "some executives"), only to be rejected. The episode was then shown to Cartoon Network (referenced as "other executives"), same thing happened. At the end of the episode, the characters mention Disney (or as A.J. calls them, "the company that brought us the happiest place on Earth"), as a reference to rumors that Disney Channel is going to pick the Modifyers up for a full series.
Mystery Science Theater 3000 - The characters are shown sitting in front of the projection screen, with only their silhouettes visible while watching the pilot, similar to Mystery Science Theater 3000.
The characters occasionally riffing is also similar to the show.
Strong Bad Email - This episode is a bit similar to the Strong Bad Email episode "best thing", which also involves a main character showing a failed pilot episode of a cartoon show.
Family Guy - Veronica having a conversation with Tootie discussing on how they sound alike (both are voiced by Grey Griffin) is similar to a scene in the Family Guy episode "Believe It or Not, Joe's Walking on Air" where Dr. Hartman and Carter Pewterschmidt have a conversation with each other, noting how they sound alike, as both characters were voiced by Seth MacFarlane, the show's creator.