Peter's cutaway to him destroying the vaccines in town is a scene in "The Dark Knight", in which Heath Ledger's character the Joker walks away as the buildings blow up. Right after, Peter also says that he needs to overdose in his apartment which is how Heath Ledger died in 2008 right before "The Dark Knight" premiered.
Sean Penn voices himself in this episode. His son, Hopper Penn, is also listed in the cast credits.
"The brothers who made the matrix are ladies now" Peter is referring to Lilly and Lana Wachowski formally known as Laurence "Larry" and Andrew "Andy" Wachowski
At the end of the episode "Bat Damon" recreates the "How do you like them apples?" scene from 'Good Will Hunting.'