These are my theories regarding the longer arc of Lost (rather than the next few episodes). I guess it contains spoilers in a sense, except that I am making the whole thing up, so I really have no idea if any of it is true.
The island is Atlantis (evidence: statue with four toes). At one point, the residents had nearly harnessed immortality, but an accident resulting from those experiments caused the island to sink (note: plot point stolen from Indiana Jones video game – Fate of Atlantis). The smoke cloud is the souls of the beings of Atlantis who were made immortal. In the video game, when the evil Nazi enemy leader guy tried the immortality device, he became a super-powerful smoke cloud demon thing. This is why we see faces in the cloud. Jacob leads the immortal cloud, but has the ability to sometimes appear?
The island re-emerged, possibly violently, creating strange magnetic abnormalities (evidence: Black Rock being in the middle of the island). This magnetic abnormality may result in healing, but also may result in difficulties in child bearing.
There is a war between the factions who know that the secret to immortality lies on the island. Possibly, The Others (or hostiles) are descendents of Atlantis. Some may even be immortal: Richard, Jacob? (evidence: Richard doesn’t age). (Soon, we’ll see Richard remove his shoes and he will have four toes.) They are working to protect the secret so that humanity doesn’t utilize it and destroy itself. In other words, The Others are the good guys.
The Hanso Foundation/Dharma Initiative was mostly a cover-up project to hide the fact that someone (Penny’s father’s corporation Widmore Labs?) was greedily seeking the secret to immortality. Perhaps some of those experiments caused the mysterious insanity/sickness that afflicted some prior island visitors. The big “surprise” down the road will be that The Others are really the good guys (evidence: Ben is always saying that they are the good guys!). The Losties and The Others will team up to protect the secret from the corporate interests (Dharma/Hanso/Widmore) who will otherwise exploit it. Naomi and her ship are Widmore people trying to locate the island. The Losties and Others will fight them.
I think the show may end with the destruction of the island via some catastrophic event and the rescue of the remaining losties/others. Ben will choose to go down with the island as protecting the island became his life purpose.
The show really needs to end with the Losties being rescued, but then it would only make sense if the island is also destroyed or impossible to find again (i.e., Sinks to the ocean floor again.)
The Others are currently off to “The Temple.” I believe this is where some secret device rests. They are going to protect it from the impending intrusion of the boat people, who were indeed proven to not be affiliated with Penny in the finale.
In the Indiana Jones video game, there is also a rare metal found on Atlantis. I suspect this metal will be the source of the magnetic properties of the island.
(VIDEO GAME SPOILERS)
Sophia is again kidnapped when they arrive Atlantis. After rescuing her from a prison and entering the second ring, it is revealed that Nur-Ab-Sal guided Sophia to Atlantis through the medallion, in order to reclaim his old kingdom. His ghost possesses Sophia completely. Indy takes the opportunity to snatch the necklace and hurl it into the lava.
In the Colossus – a huge machine in the centre of the capital, which gave the Atlanteans god-like powers, they are ambushed by Ubermann and Kerner. Kerner decides he is the most worthy one around to transform into a god. Based on Plato’s tenfold error, Ubermann feeds the machine with 1 bead instead of 10, which turns Kerner into a grotesque dwarf. The Nazis then force Indy to stand in the machine as an experiment.
Jones manages to convince Ubermann to be overpowered by anger and his own lust for power. He then feeds the machine 100 beads and turns into a being of pure energy, but soon after explodes, activating the volcano that has been asleep for millennia. As the city is crumbling, Indy and Sophia make their way to the submarine and take it to the surface. The city collapses deeper under the water, while Indy and Sophia watch the sun set on the smoke. And then they kiss.