Hi All,
Here is my theory, which dawned on me last night. I am currently watching the second half of Season 3, and it hit me like a ton of bricks while watching "one of us".
My theory does not "flesh out" all the details, rather it provides the basic "skeleton" of the plot.
If I am right, this show is essentially a huge rip-off of a movie done in the late 80s (or early 90s). I can not remember the name of the movie, but it is essentially the same as my theory below.
My theory is that there was a massive catastrophy on "earth". The Island and/or "others" are somewhere in the future. The "others" are bringing people "forward" to thier time on earth (or possibly parallel universe, or even new planet). For some reason, the "others" obviously can not reproduce and it seems "newcomers" can not without dying (this might be becuase of the "location"). The "others" are going "backward" in time, and grabbing "subjects" who would not be missed because they are dead or MIA (remember, everyone on the island "crashes" there whether by boat or plane). The "newcomers" are most like there to help repopulate the "future".
As I said, my theory is just the basic "skeleton" of the show and does not go into fine detail. Here are my facts to support it:
1) Everbody on the Island crashed there by accident.
2) They "others" keep talking about "the list" and who is on it and who isn't.
3) There are people who are "supposed to die", like Charlie who ran to the front of the plane and possibly wasn't meant to "survive" the crash.
4) The others drug "consenting" people before before the "journey", they said "it makes the trip easier". The most logical answer, is that they will somehow "die" in the present. However, the journey may be some sort sort of time/space/dimension portal.
5) Locke's "father" was in an auto accident before appearing on the Island.
6) In the last episode, Jack and Kate are obviously very distressed. My belief is because they know the world is about to have the catastrophy, with them possibly dying. Jack desperately wants to get back to the Island,a nd keeps getting on planes hoping to crash (this is where my theory of "you have to 'die' to get there" comes into play). Also, in the last episode, some people that they "know" are dying; this could be due to suicide from knowing the future, or a vain attempt at trying to get back to the island.

There is a easter egg type of video clip, which shows a Dharma official talking about a "virus" that they are unleashing on the world. This could be a few different things:
a) producing bodies to replace the people that they are grab from the "past", which goes along with the original movie I spoke about.
b) finding a vaccine for a plague which might have caused the original apolcalypse.
c) This virus is carried back to the present by Jack & Kate etc.; and Ironically, THEY cause the apocalypse.
9) The easter egg clip also dicsusses the "numbers", and says that they predict the apocalypse; so this supports my theory that the "others" know exactly when the world will end.
The only question I can't seem to work out, is who is Desmond? Why is he so central? Why can he see the future? Why does he seem to be the only one who can go back in time? (I somehow think that he holds an incredibly important key to the story)
Sorry if I am just rehashing old news, but I am a newbie to the forum. I look forward to your thoughts, as to why or why-not my theory could be true.
Thanks In Advance!