Some of the "eggs" are listed on the
Sierra Help Pages, but I (and several others) have discovered a few other references and cameo appearances.
SQ1 VGA:
The Nav-210 robot in Droids B Us is a praody of the robot from the movie "Short Circuit".
The HA-Y-AO robot in Droids B Us is modeled after the robots in the Hayao Miyazaki anime Laputa: Castle In The Sky.
When you get to Ulence Flats, right outside of the Rocket Bar, there are a few different old spaceships sort of just sitting around directly outside of it. The one furthest back and towards left/center, sort of a bluish-green generic sci-fi rocket shaped ship, is described when you look at it as "a genuine antique from the twenty-fourth-and-a-half century." This is a reference to the Chuck Jones animated short, "Duck Dodgers in the Twenty-Fourth-and-a-Half Century", and the ship in SQ1VGA does resemble the ship from the short.
Aboard the Deltaur, right after you've obtained the Sarien uniform, head up the elevator next to the captain's escape pod. Go all the way to the left, then up the other elevator. Look at the purple thing with the globe on it, and it says, "It seems obvious that Wally Wood did some time designing Sarien hardware." This is a nod to some of the retro future style artwork of artist Wally Wood, best known for having worked on MAD Magazine at one point and doing some stuff for Mars Attacks!
SQ4:
The three-breasted girl in the centerfold in Space Piston magazine (the SQ4 manual), who also appears on a poster in Singent and Nigel's apartment in SQ6, is possibly a parody of Eccentrica Gallumbits, the triple-breasted whore of Eroticon 6 from The Hitch Hiker's Guide to the Galaxy.
The Mr. Fusion feature of the Timebuster 2000 SUX (listed in the SQ4 manual) is a nod to the device of the same name that Dr. Brown attached to the DeLorean at the end of the first Back to the Future movie.
SQ5:
When Roger talks to Droole after Cliffy reports something making scratching noises in the waste compartment, Droole says, "Why don't you go back there and check it out. I'm sure it's perfectly safe", to which Roger replies, "Hmm. That must be some strange new usage of the word "safe" that I wasn't previously aware of." Roger's line is almost identical to what Arthur Dent says to Ford Prefect when Ford tells him that they have hitched a lift on of the ships in the Vogon Contsructer Fleet in The Hitch Hiker's Guide to the Galaxy.
If you look at one of the trees in the scene at the top of the cliffs on Kiz Urazgubi, its description is simply "The Larch." This is most likely a reference to the Monty Python tree identifying sketch, in which slides of various trees are shown, and a voiceover somberly names each species, with the larch being the centerpiece of the sketch.
Late in the game, when Roger tries talking to Flo, she says, "The lives of thousands of species on hundreds of worlds are depending on us, sir. [...] Humans, Xenomorphs, Rigellians, orats, even dolphins. So let's get out there and win one for the 'Flipper'." Her last line is a parody of the phrase commonly associated with Ronald Regean, "win one for the Gipper", and of course, Flipper is the aquatic star of the TV show with the same name.
If Roger runs out of fuel or oxygen while trying to rescue Cliffy in SQ5, two aliens mistake him for a shooting star as his burning craft is plummeting through the atmosphere of their world, and one alien tells the other to make a wish. This might be a parody of the Ray Bradbury short story "Kaleidoscope", where a team of astronauts is blown out into space when their ship is hit by a piece of space debris. Over the course of the story, the men slowly drift apart, and at the end of the story, the last remaining man is pulled into Earth's gravitational field, and as his body falls through the atmosphere, a mother and her child see him and mistake him for a shooting star, and the mother urges her child to make a wish.
The appearance of Genetix appears to be a homage to the research station in the film Silent Running.
SQ6:
When Roger tries touching Dr. Bellaux's posessions when he returns to Delta Burksilon V, Dr. Bellaux says one of several oaths: "By Arnold's accent", "By Losira's chromosomes", or "By Levy Shoemaker". The first oath refers to Arnold Schwarzenagger (sp), the second refers to a character from the original Star Trek series named Losira (Mortimer), from the original Star Trek, and the third refers to a comet named Shoemaker-Levy 9.
When Roger looks at one of the machines in Sharpei's room, the narrator remarks, "Cool! Another machine that lights up and goes PING!". This is a reference to the beginning of "Monty Python's The Meaning of Life", where the machine that goes PING is a state-of-the-art device that determines whether a soon-to-be-delivered baby is alive or not.
The familiar looking robot that "lacks a bit in the stature department" on Polysorbate LX is a likeness of one of the three robots from the film Silent Running, starring Bruce Dern. If you try talking to the robot, the narrator remarks, "You're no Bruce Dern, Buddy."
Everyone here knows Superman, right? Well, near the end of the game (when confronting Dr Beleauxs with the evidence) he remarks "Great Caesar's ghost!" which Perry White (the boss of the Daily Planet, where Clark Kent works) often used to say in the early comics.
If Roger tries talking to the object on the round table in Dr. Bellaux's lab, he says, "Do you understand me? Sprechen sie Deutsch? Parlez-vous francais? Klaatu Barada Nikto?" His last question is a famous phrase from the 1950s sci-fi film
The Day the Earth Stood Still.
If you try opening one of the cages in Dr. Bellaux's lab, the narrator cautions, "Hey, hey, hey, careful! These endearing little furry purring creatures have only three rules: don't get them wet, don't feed them after midnight, and...Oops, wrong endearing little furry purring creatures." The rules he starts to recite are the same as the rules regarding the creatures in the 1980s film
Gremlins.
One of the line's in the narrator's description of the bathroom in Sharpei's quarters (that quickly segues into an unrelated topic) includes the lines, "I know what you've been thinking. You're probably thinking, 'Have they waited four sequels to do bathroom humor or has it been just three?' Well, to tell you the truth, in all the sequel-generating excitement we've kind of lost track ourselves. So you've got to ask yourself just one question. Are they hard-up enough to resort to that level of humor at this point in the game?" These lines are a parody of the
Dirty Harry "Did he fire six shots or only five?" monologue.
The narrator's remark after looking at the pinup of Krille MacPherson ("Just watch that MacPherson strut!") is a blatant pun: a MacPherson strut is a form of suspension used in cars.
--from The Rudimentary Space Quest References Repository