Guitar Hero/Danny Phantom - Before borrowing Stu's guitar, Lauren had a guitar that looks similar to Ember McLain's guitar from Danny Phantom, but it's actually a guitar-shaped controller for a video game, referencing the Guitar Hero rhythm game series, where the player uses a guitar controller with a strum bar and buttons to play the notes.
The Simpsons - One of the songs that the S.I.S.T.E.R.S. made, "Smiling Politely", was named after an exchange in the Simpsons episode "Homerpalooza" where Billy Corgan from the Smashing Pumpkins introduces himself to Homer, and Homer introduces himself to Billy Corgan as "Homer Simpson, smiling politely".
Nine Inch Nails - Mercy Frank has a poster of the band Ten Inch Claws, a parody of Nine Inch Nails.
Elvis Costello/Saturday Night Live - At one point, Benjamin Woolworth warns the S.I.S.T.E.R.S. not to play a certain song in his school. When the S.I.S.T.E.R.S. perform, they play one song for a bit, then Mercy suddenly stops the music, and says to the audience "I'm sorry, boys and girls, there's no reason to do this song here.", before they start playing a different song against Benjamin's wishes, who, following their performance, bans the S.I.S.T.E.R.S. from performing in the school again. This is a reference to Elvis Costello's performance on Saturday Night Live during its December 17, 1977 show, where he started performing "Less Than Zero" before suddenly stopping and playing "Radio, Radio", making a last-minute change without notifying then-showrunner and producer, Lorne Michaels, and Costello's performance resulted in him being banned from SNL until 1989, when the ban was lifted and Costello returned as a musical guest.