In this episode, one pivotal character is named "Verona" and another character takes a drug that makes him appear to be dead but which really only knocks him out for awhile. Both of these are references to William Shakespeare's play "Romeo and Juliet": the play takes place in Verona, and Juliet takes an apothecary's drug that makes her only appear to be dead.
In keeping with the Romeo and Juliet theme going through the episode, the model car used by Walter to demonstrate his theory about how the transfer between the universes would be accomplished was an Alfa Romeo Giulietta. This model was named specifically after Juliet from Shakespeare's play.
Peter mentions that Walter wants to go to a "Star Trek" convention. Frequent Fringe (2008) guest star Leonard Nimoy played Mr. Spock in Star Trek (1966) and several other movies and shows in the Star Trek franchise, including Star Trek (2009), which was created by the same behind-the-scenes team as "Fringe."