In the first classroom scene, you can see a drawing of a flux capacitor from Back to the Future (1985) on the board behind the Headmaster (played by Christopher Lloyd, who also played Doc Brown, the inventor of the flux capacitor in the film). He also erases 1.21 gigawatts from the board at the end of the scene.
Gary J. Tunnicliffe wanted to use his knowledge and love of martial arts to create an amazing fight sequence in the movie, but knew that to do this, and still maintain a G-rating, might be hard. To solve the problem, he created a two and a half minute "Ninja Pillow Fight", and called upon some of his industry friends (who can only be described as a group of Martial Arts and Stunt Masters and Legends) to choreograph and perform the sequence.
In the pawn shop scene, Wallace Shawn offers to trade Jack Iocane powder for his C.O.W., but then decides that it is far too poisonous. This fictional powder is the same powder that led to Wallace's demise in The Princess Bride (1987).
(At around one hour and two minutes) One of the lumberjacks (played by Director Gary J. Tunnicliffe) expresses a wish to be a pet shop owner instead. This is a reference to a famous Monty Python sketch, where the reverse situation is the case.
Gary J. Tunnicliffe is rumored to have performed at least two full re-writes, and numerous polishes on the script (by Flip Kobler and Cindy Marcus), but was not allowed to take it to the WGA for arbitration.