A sketch from "Anne Marie's Pride" has the chipmunks sing with deep-sounding voices at a recording studio. Dave tries to kill them off with deadly helium and succeeds... just after he realizes the helium makes their voices high-pitched.
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A sketch from "Crushed by a Steamroller on My 53rd Birthday" has the Chipmunks engage in intercourse with groupies. Theodore and Simon are successful, but Alvin... not so much.
A sketch from "The Robot Chicken Lots of Holidays but Dont Worry Christmas is Still in There Too so Pull the Stick out of Your Ass Fox News Special" features the Chipmunks releasing an album featuring songs for other holidays, each one ending with Theodore saying that he blew a homeless man.
A sketch from "Zeb and Kevin Erotic Hot Tub Canvas" has Simon play Simon Says, which ends with him saying, "Simon Says: put your bathing suit area up against the TV screen".
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A sketch from "3 2 1 2 333, 222, 3... 66?" has Dave book the Chipmunks for Coachella.
A sketch from "Max Caenen in: Why Would He Know If His Mothers a Size Queen" has Dave kill Alvin when the latter's voice becomes too deep. Upon witnessing this, Simon and Theodore run away before Dave can kill them as well.
The fifteenth episode of the show's eleventh season is titled "May Cause a Squeakquel".
In "Homer's Barbershop Quartet", Bart finds a Melvin and the Squirrels record in Comic Book Guy's record collection.
Comic Book Guy:Melvin and the Squirrels. Part of the rodent invasion of the early '60s. Record:Stuck a feather in his cap and called it "Rice-a-Roni". MEL-VIN!
In "Homer the Whopper", a poster for "Alvin and the Chipmunks 3: Gettin' Rabies!" can be seen outside Ginormous Pictures. (This was before the official third Alvin and the Chimpunks movie was made.)