My theory right now:
Jacob is not the good guy. Everyone he touched was led astray. But, in the flash sideways we see what would have happened if they were not touched by Jacob, and therefore made more positive choices in their lives. Basically, you can't change what happens to you, but you can change how you respond to it.
Ok, I'm back. Commercial.
What about Widmore? I am not sure what to think of that. And is there more to find out about Penny and Desmond? I think Jin is a "candidate" not Sun since Sun was the only one left on the second plane crash.
I am not sure to what to make of the "infected".... Claire, Sayid. Any ideas?