Shawn asks Tom the amnesiac if he is part of Treadstone. This is a reference to the Bourne movie franchise.
First reference to "fries quattro queso dos fritos"
Pineapple sighting.
There are trays of pineapples seen during the stand off at about 40 min.
The full version of "I Know, You Know" was used in the closing credits in a number of the early episodes. In this episode, the full version of the song is used as the theme song in the opening credits. This also occurred in episode 12 of season 3.
WILHELM SCREAM: Heard as a sound effect when Tom plays a video game in his hospital bed.