So, we know Danielle had a child. People have been suggesting that Ethan is in fact Alex, but we don't know how old the kid was when they crashed, or even its sex. Ethan could have been there already. Going by the meaning of his name ("gift of the island", or something like that), he may not even have been a person, rather something created by the island (witness the scary super-strength, please?), and hell, I've been saying since they found the hatch that maybe the island isn't an island at all, rather a giant machine built to look like an island, or something like that, and that it draws planes/boats to it to amuse itself/fulfill its objective/I don't know.
We know that whatever force was behind Ethan really likes pregnant women, or maybe just babies. Now, I don't know why that is, although I have several vague, half-formed theories, but it occurs to me that, if Danielle was pregnant when they were shipwrecked, or became pregnant afterward...
...maybe Ethan, or someone from his group, also took Alex. And that that force killed/drove insane/infected everyone from her group to get to her, and/or the baby. And that she's looking at the new group of castaways thinking that it's the same situation playing out all over again. Castaways crash, island-thing notices pregnant woman, and eventually kills everyone, leaving pregnant woman (in that case Danielle, in this case Claire) alone and defenseless, at which point the baby is taken.
It's a bit out there, I know, but not impossible. Also I suspect someone else has already thought of it. But. Ooh. ;)