When deciding on a new sector to go to, Ari suggests going to LV-426, which was the name of the planet in Alien, le 8ème passager (1979).
The notepad on the back of the Vakkar corpse in the abandoned freighter had the words "Kick Me" written on it.
When Ari and Zack are discussing the Greek myth of Daedalus, who fashioned wings of feathers and wax to escape from a labyrinth, this foreshadows the following chamber where you as Casey must navigate your way through a maze of tunnels to unlock the door so Ari and Zack can escape from it.
Just before the elevator (leading from the engine room) starts to ascend, the sounds that are heard in the background are the same sounds as the Game Menu's. This sound can also be heard when the elevator is ascending and when Ari and Zack are exploring the room at the top of the elevator.
When Casey is going through the last tunnel in the maze (that turns to the left), the sounds from the Orbits puzzle are heard.