"Meet the Beat-Alls" is one long string of Beatles references.
Speaking of The Beatles, the episode entitled "Get Back Jojo".
Additionally, Him has a very similar voice to the Chief Blue Meanie from Yellow Submarine, and according to McCracken, he was a major inspiration on the character.
"The Powerpuff Girls Rule" makes as many pop culture references as it possibly can in its 30-minute timeslot. Everything from George Orwellnote Buttercup has a fantasy where she rules the world with an iron fist; an Imagine Spot shows her giant face on TV screens with the tag "Big Butter Is Watching You." to Mario Kartnote All the characters have a Mario Kart-style kart race at one point gets its fair share of homage.
Professor: No buts! I mean it! Bubbles: Anybody want a peanut?
"See Me, Feel Me, Gnomey"
The title iis a reference to the recurring "See me, feel me" lyrics from The Who's Tommy. Of course, there must have been more inspiration taken from it as well, with one specific example being a Suspiciously Similar Song to the opening of "Pinball Wizard" playing when the gnome is granting the girls' wish.
There's a certain scene in the movie with Mojo Jojo holding a newspaper headlining the girl's destruction of Townsville. The back page of the paper has a small poster for a certain ape-based virtual band complete with a heading stating that they're headlining Townsville's Music Fest. Cue Troper's head exploding after a second viewing of the film 9 years after watching it in theaters.
In the comic book "Trick or Beatings", the following exchange occurs as the Powerpuff Girls (and Mojo Jojo) are out trick or treating:
In the first Rowdy Ruff Boys episode in Season 1, Bubbles crashes through a window and apologizes to the clerk, "sorry about your window Mr. Looper." with which the clerk states "Its Hooper!! Hooper!!!".
In "Collect Her", when the Mayor is trying to determine who the culprit is, one of the name he comes up with is Genndy McCracken. This is an amalgam of two of the show's main writers, Genndy Tartakovsky and Craig McCracken.
McCracken received another shout-out in a subsequent episode in the form of a pirate names Crack McCraigan.
In "Boogie Frights", when the Boogie Man eclipses the sun with a giant disco ball, the Powerpuff Girls' final assault on the ball is an almost shot-by-shot remake of the assault on the Death Star in Star WarsEpisode IV.
An episode makes a reference to Mega Man, as two police officers ask each other who would win in a fight, Mega Man or Mondo Dude?
In "Pee Pee G's", the TV news flash graphic is similar to Kermit the Frog's live on the scene skits on "Sesame Street".
In "Octi-Gone", the professor receives a call from Mojo Jojo, who claims that he's holding Octi ransom for 1000 barrels of Chemical X. The professor asks the operator to trace the call... who reveals that the call is coming from inside the house.
In "Bubblevicious," Bubbles faces a torture device that goes Up to Eleven.
In the same episode, one of the monsters she faces in the danger room bears a striking resemblance to Spawn Malebogia.
In "Something's a Ms.", the Mayor reenacts The Big Lebowski's epically hammy "Strong men also cry" scene when Ms. Bellum is kidnapped. Later in the episode, the girls use a bag full of the Mayor's underwear as a ringer for the demanded ransom money, as Walter did in the movie.
In "The Mane Event", the villain-of-the-week is a giant sphere with one eye, resembling the Eye of Volger from Giant Robo.