Indiana Jones is a slave in a BDSM outfit.
Moses is based on the villain from this film.
mentioned in dialogue
In the opening credits, Bart's blackboard message: South Park - we'd stand beside you if we weren't so scared -- is a reference to the death threats around this episode (or actually, the next one).
Michael Palin refers to future comedians who want to make jokes about Muhammad in a bear suit.
The Super Best Friends parody this.
Mecha Streisand is a parody of Mecha Godzilla.
Rob Reiner and Tom Cruise talk about "... having her do it." similar to Gollum at the end of that movie.
Tom Cruise jumps on a couch and Oprah happens to be sitting beside him.
Rob Reiner says, "Release the Kiken."