The glyphs for this episode spell out: ALERT
The running joke of Walter having difficulty remembering Astrid's name is used again. This time he calls her "Aspirin".
Newton tells Olivia that she joined Fringe Division on September 9, 2008. This was the date that the show premiered.
When Walter Bishop is explaining to Peter and Astrid how music affects brainwaves, he uses two different songs: the classical one, as shown, from Mozart's "Marriage of Figaro". The "disturbing" rock song is, however, the main theme of the 80s TV series Miami Vice (1984).
The Observer enters the subway station just as Thomas Newton abandons the box in order to visit the lavatory.