The Observer stands behind the crowd at the Port Authority.
When Olivia is trying to convince Astrid to let her help go over Fauxlivia's files, there's a model of a molecule revolving on the computer monitor behind her. It's a model of theobromine, found in chocolate and partly responsible for chocolate causing a release of endorphins.
In the opening sequence, the main characters discuss the encrypted computer hard drive that has been accessed since last episode. Walter Bishop explains that his son, Peter, guessed the password: "It was a song lyric. Fauxlivia ruined U2 for all of us." Though it is never revealed in the episode, the U2 song in question must be "One," which has the lines "We're one, but we're not the same."
When Peter enters the house and puts down the bag he is carrying there is a seahorse on the metallic logo on it.
The glyphs for this episode spell out: ALTER