"Kirk out" is the phrase Captain James T Kirk uses when communicating with his ship in Star Trek: The Original Series.

In 3x15 "Subject 13", Elizabeth Bishop takes a young Peter to the toyshop where he looks at a board game inspired by the original Battlestar Galactica series from 1978.

In 4x19 "Letters of Transit" Walter makes a reference to this famous line from Obi Wan Kenobi in Star Wars: A New Hope.

A double reference: in 1x19, Peter and Olivia meet a conspiracy theorist who believes himself to be Spock from Star Trek: TOS. The same actor played an almost identical character in Star Trek: DS9.

Many aspects of the future presented in season 5 of Fringe are reminiscent of Ridley Scott's film, Blade Runner, particularly the night market from 5x01 and the 1940s style costuming of the 'natives'.

Two of the FBI vehicles used throughout the early seasons of Fringe have numberplates referencing robots from Star Wars: 1C3PO1 and 1R2D21.

In 5x01, an observer uses this catchphrase often used by the Borg, a species in the Star Trek universe.