
HR Giger and his baby
via smyrno
Most of you like to think of the derelict ship as a military vessel, transporting the alien eggs to infect an enemy, as part of some interplanetary war.
I, myself, preferred to think that the space jockey wasn’t transporting the eggs, but was an innocent victim, as were our heroes. I think this because the space jockey clearly had been the victim of a chest-burster, and it seems unlikely that he would have let this happen if they were his own weapon. Also, the egg chamber is way bigger than it needs to be if it were originally intended just to hold the small eggs. Also, this way of thinking makes the universe a bit bigger; it means we still don’t know where the aliens came from or who might have engineered them.
Thanks to everyone who voted!
But, from the rumors we hear about Prometheus, it seems Ridley Scott agrees with most of you guys; I think the space jockeys are gonna turn out to be not-so-friendly.

Edge of the egg chamber set for Alien. The blue lights were on loan from the The Who concert next door. The film implies the lights are a stasis field preserving the eggs. This lends credence to the idea that the space jockey was intentionally transporting the eggs, perhaps as biological warfare.
via toutlecine.com
Kane (John Hurt) descends in to the egg chamber, Alien (1979)
The blue laser lights that were used in the alien ship’s egg chamber were borrowed from The Who. The band was testing out the lasers for their stage show in the soundstage next door.