I got season 1 on DVD a few weeks ago, and watched all of the episodes again. A few things that caught my attention-
In the 1st episode, Kate says that she sees smoke and believes it is the cockpit, while they find the cockpit, could this have been the same smoke that the monster eminates?
In the 2nd episode, someone says about the "moneter" - "That sound is very familiar", and followed it up by saying she was from the bronx. I thought subway system right away. The way the 'monster' sounds like a mechanical device, like a rollercoaster, is consistant with the subway system in NY.
There are a ton of references to black and white. This seems to be a recurring theme - the backgammon, stones found on the bodies of 'Adam and Eve". This coincides with the man of science (Jack), man of Faith (Locke), and how there seems to be an imminent division between the lost-aways. The quote "I think we are going to have a Locke problem" by Jack in the last episode is very telling about where season 2 is going.
All that being said, my theory is that the hatch is a place to transport science experiments, perhaps even nuclear and industrial waste on a deserted island, but it comes with a some type of mech that picks up the 'waste', eg. people. The islanders will find that this isn't the only hatch.
Thoughts?