What happened in the Derelict ship, what caused this hole?

Yup, to me it looks like a xenohuahua got a bit excited and in its nervous state wee'd on the panel causing it to melt.  Poor xenohuahua fell through and got lost in the ship somewhere.  Until it followed Dallas and Lambert back to the Nostromo where it bacame friends with Jonesy.  See the picture below:

I think SJ gave birth to a queen.  She set up house in the map room and her egg sac penetrated the floor in order to be able to lay all those eggs below.

Perhaps the SJ was a sacrifice (as the hooded engineer in Prometheus) in order to start a new lifeform on LV-426? He would then already be impregnated with something before landing, the chest would burst as he reached the moon, and what came out (perhaps a queen) would then find a place to propagate (lay eggs) which would be in the cavern underneath the spacecraft (making a hole as she sensed there would be a perfect place there). The SJ might have been ordered to send the signal which lured the passengers of The Nostromo to land there and become the food or way to propagate for the new alien species?

The Jockey warned passing ships to stay away.

The Jockey appears fused to the chair because a merger of the biological and mechanical is Giger's primary art style. For the Space Jockey in ALIEN Giger himself said that "The creature we finally ended up building is biomechanical to the extent that he has physically grown into, or maybe even out of, his seat, - he's integrated totally into the function he performs." (Cinefex 1, p64). In addition, "The pilot is conceived as one of my biomechanoids, attached to the seat so as to form a single unit."  (Giger's Alien p34, 25 July, 1978). Source:

http://alienexplorations.blogspot.com/2008/01/dissecting-derelict-to-explain-more.html

I also agree with Chris on several points. The placement of the eggs was not random as depicted in Cameron's ALIENS but more organized; in addition, we cannot talk about the eggs without also talking about the blue containment beam covering them. The Queen did not place that beam over them, thats for sure. It's probably safe to assume both the beam and the placement of the eggs was done by the Engineers. In addition, and taking the visual evidence into account, the acid did not come from above as a result of a struggle because other structures around the hole would also show acid corrosion (they don't). The Jockey's chair, the circular platform it's on, even the immediate floor surrounding the hole look relatively unscathed, with only the rim showing some scarring and maybe traces of organic debris. As for the hole itself pointing downward and that "proving" the acid came from above... well, there's gravity. As the acid from a Facehugger below eats through the material, gravity is simultaneously kicking in and pulling everything down... so there's that.

"The placement of the eggs was not random as depicted in Cameron's ALIENS but more organized"

The only organization is that they're confined to the lower 'pit' areas of the chamber.  Beyond that, they're just as random as the placement as shown in Aliens.

SM,

Compared the two again and I agree, the egg organization is interchangeable- sorry its been a while! :)

Not at all. :)

If the jockey was attacked by a facehugger (crawling up from the cargo hold) during flight, wouldn’t the spacecraft have crash landed on the moon? Autopilot? On the other hand, if the jockey was attacked after landing, why was he still sitting there (not walking about)?

There's no way to tell if it crash landed or just landed.

Well, I suppose one might expect some damage to the ship, which we will probably find on the spacecraft that David and Shaw crash landed with.

Considering the floor is level and there's no obvious internal damage (hole in floor aside) unlike the Juggernaut, I'd side with 'landed' over 'crashed'.

In that case I suppose the only scenario is this: The Jockey gets attacked by a facehugger during "normal" flight. He wakes up in time for landing, knows something's wrong and sends a warning signal, and just when he's landed the chestburster pops out?

my theory is the engineer is facehugged in cryo sleep. once the process is over he comes to without any knowledge, like kane in alien, and believes he has just come out of cryo sleep naturally. he goes to the pilots chair to do whatever it is he wouldv done normally. the impression im given from alien is that the derelict crashes due to the chest burster erupting from the SJ's chest and that the creature creates the hole to escape/ get out of the ship possibly after it has crashed, or to find somewhere secluded to molt. the signal way be a preset warning and the SJ only had to push a single button once he realised what was happening. or again, a pre set warning for that type of ship incase of crashlanding due to the nature of its cargo. im sure the time it would take to mount a rescue the engineers would know the xeno would have established a nest and be fully grown and they surely are smart enough to avoid confrontation with that situation, so they just decide to leave it undisturbed