In WarpForce, the opening cutscene for the Bizarre Flecks war starts out with a view of the Alteon, and the words "Space...the Spinal Frontier" This is an obvious reference to the opening theme of Start Trek and Star Trek: The Next Generation.
Hans Olo is a spoof of Han Solo.
The hangar deck of the Alteon is very similar to the hangar pods of a Battlestar.
In the WarpGuardian quest where you rescue the REAL Colonel Ba'Tokk, the robot you encounter, NED-409, is an obvious reference to the ED-209 robot from the RoboCop trilogy.
Admiral Amada is an obvious spoof of Admiral William Adama.
Queen Pra'Mithia is a take on President Laura Roslin
Admiral Amada's relationship with Queen Pra'Mithia is a parody of President Roslin's and Admiral Adama's relationship with each other in Seasons 3 and 4 of Battlestar Galactica: The Re-imagined Series.
The Virtual Trainer, Tronzor, is a spoof of Tron.
The FarGate quest is a parody of StarGate.
Ensign Fisher is a spoof of Carrie Fisher, who plays Princess Leia in the original Star Wars trilogy.
Lieutenant Roddenberry is a parody of Gene Roddenberry, the creator of entire Star Trek franchise.
Finception is a parody of Inception.
The Find Ken Benobi quest is a parody of the first several scenes of Star Wars Episode IV: A New Hope.
Starship Snoopers, and the monsters encountered in the quest, is an obvious reference to Starship Troopers.
The Gravity Anamoly quest
The Zhoom 6000 could be a take on the Viper MkVII
Ken Benobi is a reference to Ben Kenobi
The I.G.S. Collolisk is a spoof of the Death Star.
The 74NK looks very similar to a Cylon Centurion from Battlestar: Galactica
Arty Dedeux is a spoof of R2D2, and the armor that Arty uses when he fights against you looks a lot like R2D2
The Virin Infection quest could be a parody of the Battlestar: Galactica episode where a Cylon logic bomb virus threatens to cripple Galactica.