The episode, "Raisin the Stakes" contains multiple subliminal messages. DNA Dan, the school's mascot, appears saying, "Let's Go to the Dark Side." At the PTA meeting, when Principal Scudworth starts talking, a picture of him and the words "Scudworth is you're favorite character!" flash across the screen. After the first commercial break where many of the characters are sitting in JFK's van smoking raisins, a picture of an anthropomorphic raisin smoking a "human doobie" can be seen in one frame. When JFK is sitting in his wheelchair with a broken leg, the message, "I Buried Ponce" flashes across the screen (a reference to the phrase, "I buried Paul", which can allegedly be heard at the end of the Beatles' "Stawberry Fields Forever"). As Ghandi and the dragon fly over the school at the end, the phrase, "For more information about raisins, consult your local library" flashes across the screen.
All five of the main characters are a clone of a historical figure that met with a violent death: Lincoln, Gandhi and Kennedy were assassinated, Joan of Arc was burned at the stake and Cleopatra committed suicide by snake bite.
In "Raisin the Stakes", JFK's incoherent mumbling after falling through the skylight is clearly normal speech played in reverse. When recorded and re-reversed, he says: "I am talking backwards, and telling you to watch Clone High... and for us to win an Emmy... I'm saying that backwards... 'cause it's sneaky!"
In the script for the pilot, Mr. Butlertron was named "Mr. Belvetron" and programmed to take on the characteristics of movie/sitcom character Mr. Belvedere from Mr. Belvedere (1985), which is the reason he calls everyone "Wesley" (most noticeably Ghandi).