Lots of Lost Types on the Island Theory by LostKat

The island is a "mystery spot" on earth that has electromagnetic anomalies and perhaps other powers having to do with the alignment and movement of the north and south poles. Over eons of geologic time, the poles have shifted and left behind places that are haywire. Dharma, searching for ways to affect the Valenzetti equasion, discovered that the magnetically powerful island existed and went there to conduct experiments, funded by Hanso and Widmore. Unbeknownst to them, many, many human travelers have been accidentally sucked into the island for hundreds, maybe thousands of years. The Black Rock, Adam and Eve, etc. When Dharma researchers arrived with their supplies and computers and experimental animals and germs, they encountered a society (or societies) of descendants of these various ancient survivors, with a unique, strange, isolated culture. (Four-toed statue? Think Easter Island.) Dharma had to make friends with them and win them over, like Cortes and the Aztecs, but the existing islanders had no defenses against Dharma's natural germs and viruses. Finally there was all-out war among the factions (The Incident), Dharma was unable to keep their magnetic experiments under control, and they had to fortify themselves in locked hatches and other fortresses.

Those who survived the virus are sterile. When newcomers hit the island, the children are taken because they have strong antibodies from routine immunizations. They didn't take Claire to inject her baby and "save" him, they EXTRACTED something FROM the baby (that looked like an amniocentesis needle) that they needed to keep producing vaccines.

There's a lot missing from this theory but it's evolving!
Theory by LostKat