Though on the point of losing interest in Lost, here's my theory:
"Lost" is loosely, but conceptually based on the 50's sci-fi movie "Forbidden Planet." One can find a synopsis of the plot of Forbidden Planet on the Internet, so I won't bore you here with it. However, for me at least, the themes of the two stories appear to have some resemblance to each other.
Forbidden Planet involved an ancient alien race, now long gone, that had created an advanced subterranean technology which could physically manifest ones thoughts. Such a technology could be useful (e.g. creating food), or a playful diversion. However, for the creators of the technology, the unforeseen downside of the technology was that it would also manifest other, more dark thoughts involving fears, envy, hate, guilt, greed, etc., which linger in the mind. This darker aspect led to the unintended self-destruction of the ancient race.
If this theory is correct, then deep below the island is the hidden technology - all that remains of the ancient race. The "others" are the remains of a scientific group sent to study, and potentially harness the technology. This might have been done through the use of unwitting subjects placed on the island in the hatches, etc., in order to observe the effect of the individuals on the island (i.e. the technology), and vice versa.
However, in the end, the "others" were overcome by the same darker aspects of the technology which led to the collapse of the experiment - and possibly led to the island being placed under quarantine from the outside.
I won't go into all the implicatios for some of the subplots, this theory seems to explain the excessive use of flashbacks by the writers - that is, it reveals the state of mind of the individuals and why the survivors often see individuals from their past, etc. I seem to recall the little boy had a magazine with polar bears on it, and then we discover the island has polar bears.
What is the "smoke monster" for example? In this theory, it is no more than the physical manifestation (created via the supertechnology) of someone's darker thoughts. So, for example, Eko could have been killed by his own guilt and inner 'demons', or perhaps by as of yet to be revealed malevolent individual.
Theory by RTREACY86@AOL.Com