When Agent Dunham walks out of Massive Dynamic and meets with shapeshifter Agent Francis, The Observer may be seen in the foreground.
Peter Bishop specifically mentions watching Invasion of the Body Snatchers (1978) when he was younger. Leonard Nimoy, credited with a "special guest appearance" in this episode, starred in the film as Dr. David Kibner. Another guest character in this episode is named Rebecca Kibner.
The glyphs for this episode spell out: MEMORY
This episode features the running joke where Walter can't quite correctly recall Astrid's name. Here he calls her 'Aspirin'.
The effect used on Leonard Nimoy's voice while he was talking with Olivia in memory was used again by another J.J. Abrams production, Star Trek (2009), when Spock Prime, also played by Nimoy, tells Kirk about how he ended up in the alternate timeline. This episode and the movie were released in the same year.