The game was made during the run of the series.
The episode guest stars Ben Browder, the lead from Farscape and the DJ is named Scorpius, the name of Ben Browder's nemesis in Farscape.
When John is being interrogated after being recrystalized, he recounts his story using the dialogue from the tv series' title sequence "My name's John Crichton..."
mentioned by WIllis
During the fight in which Flynn dies repeatedly, he says "Frell!" one of those times. Frell is a word used in Farscape as an expletive.
Abed discusses the show with a man in the bar
mentioned by Ed
Jenna Marshall uses the name Aeryn Sun in the online game Black Forest 2
Sam says "Frakking Frell"
One of the possible answers to the question "Xander, Willow, and Oz were all characters on..." in the age verification form is "Farscape".
Seen On TV (28:30)
10 min section about the series
A segment has members of Stargate play and parody Farscape.
The Space Weaver is a homage to Moya's Pilot.