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At the end of the episode, Manson's jail cell has books on a shelf created by him, and one was called "Are you there God? It's me, Manson" which is a reference to the book Are You There God? It's Me, Margaret.
Manson's forehead swastika, after his change of heart, is replaced with a happy face. During the car chase, it also briefly turns into a Visitor.
When Uncle Howard decides how to escape the police, he says, "We're coming out through the bathroom window," a variation of the title of the Beatles song "She Came in Through the Bathroom Window".
They never refer to Manson as "Charles", the name he's better known as, just "Charlie", most likely for the sake of the Charlie Brown parody.
Manson steals Cartman's grandpa's car. Before the famous murders, Manson did time in prison for stealing cars.
Before the murders, Manson tried to make it as a singer/musician. His big musical number may allude to this.
Manson's jail shirt has the ID number 06660, similar to 666 a reference to the antichrist or satan.
When Cartman wakes up after his uncle and Charlie Manson break in, he is wearing a 'Beef Cake' t-shirt, referring back to the episode "Weight Gain 4000".
When Manson takes the boys back to the Cartman home, there is a news reporter named Robert Pooner, a name that appeared in the beginning of "The Spirit of Christmas", the original South Park short made by Matt Stone and Trey Parker.