My predictions:
The "Hostiles", or original inhabitants of the Island, are a group or series of people who, over the centuries, have managed to become stranded on the Island...i.e. the Black Rock and discoveries of equipment and items from various time periods on the Island sugges this.
The Island has special metaphysical properties which cure disease, perhaps provide immortality, etc. Jacob is perhaps the oldest inhabitant of the Island, and has somehow merged with the Island, and is now perhaps one with the Island.
The Dharma Initiative/Hanso Foundation somehow finds out about the Island, and wishes to harness the powers of the Island...hence the experiment stations...I believe that Dharma at one point conducted experiments on the inhabitants of the Island, and at some point they revolt, culminating with the purge enabled by Ben.
Now why Ben is special? Because he is an outsider who is able to communicate with Jacob...perhaps the other "Hostiles" have been unable to communicate with Jacob, and because Ben can, he assumes a sort of prophetic leadership role.
The Hostiles maintain the stations...Mikhael wearing a Dharma uniform, etc...because they don't want the Dharma initiative to learn that they have revolted and taken over the Island...that is why the Dharma food drops keep coming...that is also why the Hostiles are able to seemingly come and go from the Island as they please, or at least Ben's inner circle can.
Now because Ben is a friggin nutjob, he has chosen to abuse his power...somehow managing to imprison Jacob, and control the Hostiles to do his bidding.
When the Losties show up, it threatens Ben's primacy and also what he is apparently hiding...I suspect the role of the numbers, fate and destiny will play into how all of these characters, with seemingly connected lives, end up on the Island...the Island may play into some sort of space/time continuum power where it can control fate and destiny...not a concrete theory, but the only thing I can think of for now.
When Locke manages to blow up just about every station on the Island, he also allows the Dharma Initiative to catch wind of the fact that something isn't quite right. The freighter, and Naomi, are representatives of the Dharma Initiative.
Now why does Naomi have a picture of Desmond? Because somehow, Penny's father, and I suspect Sun's father and Jack's father, are either members of the Hanso Foundation or Dharma. Could explain why so many of the Losties have seemingly powerful or influencial people as parents or acquaintances. Naomi gets the picture from Penny's father, not Penny.
Penny is on the other end of the Looking Glass station, sending a transmission, because she somehow finds out from her father where Desmond is...and is trying to contact him.
I suspect next season, we will see the Dharma Initiative show up in force. I suspect that Locke, who is now able to communicate with Jacob, and was perhaps saved by Jacob, will ascend as the leader of those who wish to protect the Island. Those on the Island will splinter between those who are loyal to Locke/Hostiles/Others/want to remain on the Island and those who want to get off the Island.
I think Jack and a few of the Losties will sell out the Locke camp big time to escape. This is why Jack is such a mess in the flash forward sequence...maybe he does it out of love or pride or whatever, but I have a feeling we are going to see a huge body count next season.
I believe the season finale was a flash forward...Jack had visions of his father in the first season on the Island...I suspect that Jack's father is not dead, or that he will come back to life through the powers of the Island...Mikhael has seemingly died twice now, and has come back from the grave...Walt is now seemingly running about the Island...etc.
Why Jack says his father is upstairs...this was to show that either Jack has truly gone insane, or because his father IS alive, and it will play into his escape from the Island. If my theory is correct, and Jack's father is a member of Dharma/Hanso, then maybe Jack's father allows Jack and a select few to leave the Island...the rest are held there against their will...hence Jack's remorse, and Kate's attitude towards Jack in the future.
As for the person in the coffin...screen shots show that the person in question was from New York, and their name starts with a "J". Could be anyone at this point...Ben is the obvious choice, with Sawyer, Michael or Walt as other guesses.