The Powerpuff Girls Movie: Mojo raises an army of genetically-enhanced simians and says he will be "king of the planet of the apes". A little later, Buttercup shouts to a gorilla "Get your hands off him, you darn dirty ape!"
Rugrats Go Wild!: When Angelica finds her Cynthia doll washed up on the island, it's in the same half-buried pose as the Statue of Liberty from the film.
Spaceballs: Near the end, the Mega Maid falls onto a planet's beach. Two intelligent apes notice the villains climbing out of the half-buried ship, which is now posed like the Statue of Liberty, and one of them bemoans "Oh, shit. There goes the planet."
Sheldon: This strip, part of a storyline in which Gramp reveals to have bought seventy-five boxes of razors in preparation for Y2K, has him admitting that he thought the razors would save him as human civilization crumbled. What possible scenario did he have in mind?
(Imagine Spot of Gramp in a net, wielding a razor over Dr. Zaius and two other apes)
A cutaway from "I Am Peter, Hear Me Roar" shows Peter making an insensitive joke while at the apes' mercy.
In "Road to the Multiverse", Brian and Stewie ends up in an alternate reality where dogs keep humans as pets, and Stewie says to Brian, "Get you stinkin' paws off me you damn dirty dog!"
A cutaway from "Quagmire's Quagmire" shows Peter taking his sweet time ordering at a fast food restaurant; bu the time he's made his decision, Earth has become a post-apocalyptic wasteland populated by apes.
Futurama: In "The Laten Philip J. Fry", Fry goes further in time and looks at the ruins of New New York. He breaks down at the sight of a series of Statues of Liberty, showing that mankind, apes, bird, cows and slugs destroyed their societies.
In "Deep Space Homer", Homer says at a NASA press conference that he hopes he never goes to the Planet of the Apes... only to realize 30 years too late that it was Earth All Along. He proceeds to reenact Charlton Heston's breakdown, humiliating the NASA officials.
In "Bart's Girlfriend", the scene of the town's parents hunting their wayward children spoofs the human-hunting scene.
In "A Fish Called Selma", Troy McClure stars in a stage musical based on the film, called Stop the Planet of the Apes, I Want to Get Off!.
In "Pulpit Friction", the montage of bedbugs spreading through Springfield spoofs the ending to Rise of the Planet of the Apes. One shot even has Eddie and Lou fighting a monkey on horseback.