I think that Claire's baby died in the plane crash - in the first episode or two, she said that she hadn't felt the baby move since they had crashed. Then she ate some of the food that Jin scrounged from the ocean and suddenly the baby moved again. I think the island "granted" her wish for her baby not to have died.
Charlie wanted his guitar - the island gave it to him.
Locke wanted to walk again - the island gave back the use of his legs. And then, started to take them away again as a test of his faith and dedication. And when he passed the test, he got his legs back again.
Kate wanted to be free of the ranger - and he died.
Boone wanted revenge on Shannon (but did he really? he had a love/hate relationship with her so he didn't want any real harm to come to her) and the island gave him the "vision" of her being torn to pieces - and it freed him from the hold she had over him.
Hurley wanted food - and the island gave Locke a boar to bring home to everyone.
Sawyer wanted to be free of the guilt he felt for what happened to his parents, and from the guy he shot in Australia, and believed a boar was messing with him as a result. He went after the boar, found out it was a baby, and found some peace in letting it live.
Locke said that Boone's death was "a necessary sacrifice" that the island demanded.
All of that is to say that I think the island is somehow using the survivors as an energy source, feeding off their emotions, guilt, desires, etc., and giving a little to them while asking for a sacrifice in return from them when it "needs" something. Whether it's the island itself doing this, or the monster/security system (what is it protecting? the hatch?), or the "others", I don't know. But the taking of children has been a recurring theme - first Danielle's baby, then Claire's baby dies but is brought back to life again (because the island needed it alive?), then Ethan tries to kidnap Claire (so that the "others" could take her baby when it was born?), then Danielle takes her baby (and tried to get to her before it was born as well), then Walt is taken.
On second thought, maybe all that was to say that I really have no clue what's going on.
I'm leaning toward the scientific experiment theory. Since Walt has "special" powers and everything happening seems to be pretty mystical, I think there's a lab in the hatch (scientists? aliens? either one works for me) and they are doing experiments on... children? Castaways? Emotionally fragile paraplegics? I dunno!
