As the series approaches its end, fan speculation on just what is going on is as hotter and heavier than ever. Most intriguing is the nature of the entities known as "Jacob" and his nemesis, the "Man In Black" (MIB).
Most fans assume that Jacob is "good" while MIB represents "evil", but I think the writers have returned to their Season One roots and are presenting characters who we will totally reevaluate after seeing their back stories.
I think Damon and Carlton's notions of good and evil are much more subtle than audiences are used to. The nominally "good" Jacob has interfered in hundreds of lives and caused untold death and destruction. Jacob is fond of telling people "they have a choice" but he's engineered their lives so their free will leads them to a predetermined destination. Jacob in effect subverts free will and enforces predestination.
LOST promotional materials leading up to the final season went out of their way (it seems to me) to call LOST a Sci-Fi show. The show's history includes a strong sci-fi element that has yet to be addressed this season - the Hanso Foundation and the DHARMA Initiative. I think it's likely that we will find Jacob and MIB are the victims of DHARMA experimentation with life extension and time travel. Or at least we'll be given some reason to believe that. I wouldn't be surprised if their ultimate origins were never clearly deliniated.
What if you were once a man, but with unlimited lifespan, caught in a loop of time watching events unfold over and over (like in "Groundhog Day"). How would you amuse yourself? Perhaps by watching peoples lives, After that got tiring you might try interfering in subtle ways and seeing how it changed the outcomes of that life each time. And after that, you might try directing a life to a specific outcome. Finally, you would direct the lives of many, interweaving them into a tapestry. You have all eternity to get it right. Saying the right thing at the right time; handing a pen to an angry young boy; allowing a girl to get away with stealing. It doesn't matter if someone gets hurt. They'll be OK in some other incarnation.
Jacob is evil.