The scene where Morgan walks on the thumb tacks with bare feet, goes to scream out, then quickly covers his mouth with one hand while hopping is almost identical to a similar scene in the MGM cartoon "Deputy Droopy" from 1955.
After getting the Intersect back, Chuck says, "Guys, I know kung-fu." In The Matrix, Neo says "I know kung-fu" after he gets the knowledge of it uploaded into his brain.
Barefoot and wearing a white tank-top, Morgan crawls through the air vents when gunmen take over the Buy More. He then tries to save Casey, Jeff, and Lester by taping a gun to his bare back, and says "Yipeekiyay," when he tries to pull it.