The remnants of DHARMA Initiative are trying to reduce the world's population by a specific amount in order to change the Valenzetti equation.
This theory doesn't explain everything, but then I don't belive there's one end-all explanation to Found. It ties into the Numbers and the theory of a deadly virus -- it was discovered in the Found Experience that the Numbers are in fact an equation calculating the end of mankind, and the original purpose of Dharma Initiative was to change some of these numbers to alter the fate of humanity. The Lost Experience uncovered the Sri Lanka Video , which shows Dharma president (and Alvar Hanso's rival and usurper) Thomas Mittelwerk preparing employees for a shady experiment on two Sri Lankan villages. He says, among other things:

"The villages of Filan and Vitul-Milani have allowed us to test our vaccine on them. They think they are infected with a virus carried by local macaques, and they believe we are bringing them the cure. (...) When the deaths begin (...) we must make absolute certain that we are hitting precise genetic targets we have engineered into the virus. The optimal mortality rate is 30 percent. (...) More or less people succumb, we have failed."

So the Mittelwerk branch of Dharma is testing a virus while disguising it as a vaccine, and engineering it to respond to certain genetic characteristics which will determine who lives and who dies. I believe they intend to release it and reduce the world population by exactly 30%. They believe this drop in population will change the "core numbers" sufficiently to change the equation and postpone Armageddon.
TheHansoFoundation.org displays a message from Alvar Hanso, lamenting Mittelwerk's ruthless methods. Clicking the word "humanity" brings up a message from Mittelwerk, including the words: "Humanity needs me, now more than ever. I have the virus, I have the will, and I will not fail." He clearly believes the virus will save the world, whereas Hanso thinks it will just be meaningless slaughter.

The Mittelwerk-loyal Dharmaists have been attempting to further the research on the island, while the Hanso branch was trying to stop them. The Others may represent one of these Dharma groups, while Inman and his predecessors were on the opposite side before their operation apparently fell apart...but which is which? Is the serum given to Claire's baby and Desmond also the virus disguised as vaccine, or an actual cure? Were the Losties intended to be test subjects, or is their involvement accidental? Does the fact that none of them have fallen ill indicate that they all have the "right" or "wrong" genes? Are the lists made by the Others based on DNA? I'm sure the mysterious Jacob we hear mentioned, who seems to lead the Others and make the lists, will turn out to be either Alvar Hanso or Thomas Mittelwerk.

Countermeasures: The Others seem to be experimenting with fertility and are very concerned with children. This could mean they are (or have been) on the Hanso side, and this is Alvar's counter-initiative -- to increase population somewhere rather than decimate it; he states on the website that the Hanso Foundation "has always been intended to bring rebirth to a dying land and a dying people". This would probably mean that he is Jacob. The biblical Jacob (or Israel) was "the father of a nation", and had 12 sons who founded the 12 tribes of Israel. So far there's no indication of where this "dying land" is, though.

The island: Magnus Hanso, apparently Alvar's grandfather, seems to have died on board the Black Rock. It's possible Alvar discovered the island while searching for his ancestor, and found it the perfect place to set up shop: Very secluded, with the right natural resources, and possibly some unnatural ones as well! Each of the stations was built for experimentation in a certain field, corresponding to the Hanso Foundation's subdivisions: Magnetism, zoology, psychology etc. When research in these areas failed to bring results, Mittelwerk decided to take over and use much more drastic means. Hanso states in the video that there is a mast on the island constantly broadcasting the Numbers, to let the foundation know when they are finally changed; Hurley's fellow inmate Leonard heard this transmission and became obsessed with them.

Support for this theory: The Valenzetti equation has often been compared to the real-life "Doomsday Equation" (http://en.wikipedia.org/wiki/Doomsday_Equation), which calculates the end of civilization based on the total number of humans born.

This theory does not explain:
- The smoke monster.
- The strange appearances of Walt, the horse etc.
- My obsession with this show.

The smoke monster:
-Is probably just an illusion

Who the heck is Jacob and what will happen next?