When leaving Ulence Flats, the time pod from SQ4 pops up.
The droid in the Deltaur's armory is Marvin, the ever-popular
superintelligent paranoid android from The Hitchhiker's Guide to
The Warbird from Star Trek appears in the intro and when
you choose the wrong coordinates for your ship three times.
The closet door in the Arcade shuttle bay entrance bears the logo of
a sword through a planet - used by the Alternate Federation in
Star Trek: Mirror Mirror.
When entering the hologram area on Kerona, the theme song
starts out like the theme song from "2001: A Space Oddysey", but
then changes into something different.
When you press the "don't touch" button in the escape pod,
you end up at Nottingham Castle, featured in "Conquests of Camelot".
The storedroid working for Droids-B-Us is Robbie from
"The Forbidden Planet".
The Blues Brothers, ZZ-top and Madonna appear in the
bar at Ulence Flats.
The nose of a Star Trek: TNG shuttle is sticking out
from behind the bar.
The Xenonian man that awards you with the Golden Mop at
the end of the game is King Graham from the King's Quest series.
Droids-B-Us is a parody of Toys-R-Us. There's even a
modified version of the Toys-R-Us giraffe in front of Droids-B-Us!!
At Ulence Flats, look at the mountains in the distance.
YoWammy National Park is mentioned. This is a parody of Yosemite