This title is a reference of Hannah Montana. The "Banana" in the title is referring to the Evil Monkey.
Chris with "HATE YOU" on his eyelids parodies a scene in Raiders of the Lost Ark when a girl in Professor Jones class has "LOVE YOU" on her eyelids.
The A+ paper Monkey wrote for Chris is called "The Slave Trade Allegory of Curious George", a reference to the book series. The allegory is the fact that a white man takes a monkey from Africa and brings him to America.
The scene where Stewie blackmails Brian by subjecting all of Brian's siblings to a horrible death is said in the commentary to be a reference to the SAW films and general sadistic horror.
After Stewie reprograms the Miley android, making it go haywire, the android shouts "Miley smash!". This is a reference to The Incredible Hulk.
The ending is a parody of King Kong, only the roles are reversed. Instead of a primate grabbing a beautiful woman to the top of a building, it's vice versa.
The scene where the monkey falls off the building and gets saved resembles The Matrix Reloaded, where Neo saved Trinity in the same way.
When Miley is shot on the top of the building, her skin shreds to reveal herself to resemble The Terminator. This continues when she plummets from the roof and is dead, with her red eye slowly going out. When she destructs, only her arm is left as in the film.
Chris uses two logs to crush Peter's head while they are mad at each other. The camera angles are reminiscent of Return of the Jedi when the Ewoks use two logs to crush an AT-STs head.
Chris tries to lure the monkey with "free monkey seed." This is a regular gimmick used by Wile E. Coyote in the Warner Bros. Road Runner cartoons.
Herbert paints Chris in the exact same pose as The Birth of Venus by Sandro Botticelli.