There's a small signature "Crowe" located in the game intro, referring to Mark Crowe, one of the game designers and the artist of the game.
There's a TIE fighter (from Star Wars) in the junk freighter. It's been renamed to a bow-tie fighter from the cologne wars (as opposed to the Clone Wars in the Star Wars movie). Also the ship Jupiter 2 from the old "Lost in Space" series is located there.
Arnoid the Annihilator android is a spoof on Arnold Schwarzenegger as the Terminator.
Fester has a postcard from Arrakis in his shop. Arrakis is the planet from the game series and movie "Dune". Also check out the other postcards.
When you first arrive to Monolith Burger, the USS Enterprise (from the original series) is docked and then warps away.