In the short, "Potty Emergency," the name of the spaceship on the movie screen reads "MST-3K." This is a reference to the parody show, "Mystery Science Theater 3000," which often showed movies that would've looked as thrown together and cheesy as this one.
During the "Sir Yaksalot" sketch, the Warners lead King Arthur into the war room where a conference is being held to determine how to deal with the dragon. The table is filled mostly with Japanese scientists and generals in reference to the many Godzilla films. To further this reference, Raymond Burr (as Perry Mason) is also present. Burr was in the Americanized version of the first Godzilla film, Godzilla, King of the Monsters! (1956). Also at the table (even though he has no spoken lines) is Dr. Strangelove from Dr. Strangelove or: How I Learned to Stop Worrying and Love the Bomb (1964). (Godzilla is believed to have been awoken by a nuclear bomb.)