First off, this all begins with how the show begins: Jack in the jungle, far away from the crash.
Now I believe what we are seeing right now is two alternate realities bridged by the Island and it's properties. If you're a Lord of the Rings fan, think of it as the Gray Havens, not everyone can use this bridge, hell not even everyone can find the island. I also am a firm believer that the island is a time loop, this evident from the man in black's 'it always ends the same'. Jacob brings people to Island to prevent the end. That end being the Island being underwater.
Okay, now that that is out of the way, I'll get down to business. I believe everyone dies except Jack. Sayid was important to keep alive for Jacob as Sayid dies playing out Jacob's victory. His victory being either death or contined entrapment of the MIB, I'm thinking death. Jacob, who still has firm ties to the Island appears to Jack, who is relieved it's all over as Christian (in white shoes) and tells Jack he thankful, offers him a reward. (This is also what I believed happened to Richard. I believe he trapped the MIB, and his wish was to live on the Island forever and Jacob granted that)
Jack's wish? 'I want to go back'. The cut on Jack's neck is a serious clue, his realization of it is his proof that it all actually happened. Jacob switches the two Jacks causing a Schrodinger's cat effect, with both possibilities happening, and two realities created. Desmond can ride the bridge between these two realities, though his presence of the plane makes me feel he wants to change things, which confuses me. It also conflicts with another theory I have. Of course I think Juliet saying 'let's go for coffee' will be said again, to Sawyer as well. Of course there's holes, it's Lost. This was just my incomplete idea :)