When Roland Armitage (Barry Bostwick) calls Audra "Janet" and is corrected, he promptly says "Dammit". Barry Bostwick sang "Dammit Janet" in Rocky Horror Picture Show.
The song Buzz sings in the beginning of the movie is a song by The Friendly Indians (show creator Steve Franks's band that made the theme song).
The music playing when Shawn performs for Yang in The Chief's office is the tune of "Dazzle and Stretch" from season 1 episode, 5 "9 Lives".
At the beginning of the show, Spencer tells Gus, "Don't rain on my parade". This is a reference to Funny Girl.
Shawn tells Gus, "Don't be the model of a modern Major-General." This is a reference to the opera Pirates of Penzance by Sir Arthur Sullivan MVO.