In season one, episode nine, "The Dreamscape", the victim that fell from the Massive Dynamics building had a flight booked on Oceanic Air to Omaha, the same airline featured in Lost (2004). Oceanic Air is a fictional airline used in several Hollywood productions where bad things happen to aircraft. (Real airlines are understandably reluctant to be associated even with fictional crashes and hijackings.) It goes back at least to Executive Decision (1996) with Kurt Russell and Halle Berry.
In season one, the Fringe team has several encounters with a man named David Robert Jones. In the second season, they fight a visitor from the alternate universe named Thomas Jerome Newton. "David Robert Jones" was David Bowie's real name, and "Thomas Jerome Newton" was the name of the character he played in The Man Who Fell to Earth (1976).
Jasika Nicole has said in several interviews that the Alternate Universe version of her character, Astrid, is on the Autism spectrum (or has high-functioning Asperger Syndrome), which accounts for her statistical prowess and her disinclination to make eye contact with others. Nicole has said that her inspiration for the character comes from her own sister, who is also on the spectrum.
For the first season, each episode of this show ran from about forty-nine to fifty-one minutes in length. This is in contrast to the typical forty-two to forty-three minute length of a one-hour drama. This was an experiment by FOX to see if viewers are more likely to tune in if there are fewer commercials.
During the DVD commentary for season two, episode twenty, "Brown Betty", featuring Effects Supervisor Jay Worth, co-Producer Tanya M. Swerling, Composer Chris Tilton, and co-Music Supervisor Billy Gottlieb, they discuss the fact that every episode of this show includes an "Easter egg", a reference that foreshadows some element of the next episode.