Shawn tells Jules that "Gus isn't going to end up robbing a bank in a beret with a machine gun." This is a reference to Patti Hearst, who was abducted by the SLA, and robbed the Hibernia Bank in San Francisco.
Lassiter calls Dot, "Squeaky Fromme". This is a reference to Lynette "Squeaky" Fromme, a member of the Manson Family. Squeaky attempted to assassinate President Gerald Ford and was sentenced to life in prison. After 34 years, Squeaky was released from prison on August 14, 2009.
The exchange during the "Barn of Truth" segment, when Eli asks Milosh for the gourd but is instead handed the man's left shoe, is a reference to the "schism" scene from Monty Python's Life of Brian (1979).
The copy of the "Simplicity Pledge" Shawn finds while snooping through Eli's desk drawers is signed "Black Beard".
Spot the Pineapple: there is a pineapple shaped towel holder at the organic fruit stand.