His characterization as a genius-level evil ape fond of excessive gesticulation is based on Dr. Gori, the antagonist of antoher 70's toku, Spectreman.
Allegedly, one of the main inspirations for Mojo Jojo's speech patterns was DC's Superdictionary. The same one which included the memetic Luthor stole 40 cakes image.
In "Super Zeroes", The Mayor has a Jigglypuff Watch.
Also in "Super Zeroes", Buttercup's comic book "Spore" is a direct parody of Spawn, complete with a Malebolgia expy granting her powers.
In "Cootie Gras", the montage showing Mojo's rise in the world of organized crime directly parodies scenes from The Godfather and Scarface. He even channels Don Vito Corleone during his An Offer You Can't Refuse speech at the mayor. Also, a painting of Mojo and Harry Pitt is similar to that of Tony Montana and Elvira.
"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.
In "Twisted Sister", the Professor's book detailing the creation of the girls is entitled "How I Did It".
"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 is a reference to the recurring "See me, feel me" lyrics (and the eponymous song) 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 "It's Hooper!! Hooper!!!".
In "Collect Her", when the Mayor is trying to determine who the culprit is, one of the names 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 named 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 Death Star trench run 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, a subtle shoutout towards the movie This Is Spinal Tap and the infamous going up to 11 scene.
In the same episode, one of the monsters she faces in the danger room bears a striking resemblance to Malebolgia.
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. This was most likely one of Lauren Faust's contributions, as she's a huge fan of the film.
In "The Mane Event", the villain-of-the-week is a giant sphere with one eye, resembling the Eye of Volger from Giant Robo.
In "All Chalked Up" HIM convinces Bubbles to draw chalk monsters to "express her anger" and brings them to life. One of them is a giant turtle a la Gamera. it doesn't have the tusks though..
In "Roughing It Up", the Professor and the girls are at one point panting nature paintings together, and while they do, the Professor sounds and acts like famous TV painter Bob Ross and is even painting a similar mountains-and-trees landscape. To drive the point home further, his head is partly obscured behind a leaf-covered branch making it look like he has an afro.
A roundabout one: the show's original title was "The Whoop-Ass Girls," inspired by a friend of Craig's who always used the phrase "open a can of whoop-ass," but he only officially decided to use it when he misheard the lyric "My roof has walls" in The Pixies song "Nimrod's Son" as "My whoop-ass balls."
The Blossom's first fight with Princess Morbucks is a scene-for-scene shout out to Dragonball Z. The energy blast, the Nonchalant Dodge, the smoke, and the fight between the two were directly from one of the fights in the Namek Saga.
In "Beat Your Greens", a large boy is wearing an NWO shirt.
In the Polish dub, Keen on Keane is named Ken i Keane (Ken and Keane). Barbie, anyone? It also fits the episode's plot quite nicely.
In a meta example, the Hanna-Barbera logo used during the first 3 seasons is the one they used during the 80s-specifically the CGI Swirling Star- rather than the "character portrait" logos they were using at the time. Since Craig McCracken grew up during the 70s/80s it was likely intentional; although it probably became a Harsher in Hindsight moment for Craig when he learned that PPG would be the studio's final TV series (the Cartoon Network productions were split off into Cartoon Network Studios, while H-B's remnants were absorbed into Warner Bros. Animation).