There is likely little need to elaborate on the major dichotomies of Lost, as they have been well documented in other theories. One important component is the consistent reference to ancient civilizations (most notably Egyptian), and archetypes/conflicts that are very referential to the Torah/Old Testament. One idea about the role of MIB-Jacob is yin-yang and duality, both must exist and serve specific roles. An excellent theory on the message board here discusses roles of Creator-Destroyer-Maintainer (or something to this effect) which are underlying themes of mythology.
In ancient civilizations, black and white were often represented in the casting of stones to make decisions in both trials and other important cultural/tribal decision makes (i.e., casting lots). Black rocks were an indication of condemnation or rejection while white rocks were an indication of acquittal or acceptance. We've seen black and white stones in multiple places, namely, the backgammon pieces, Adam and Eve, and most recently the stones in MIB/Jacob's cave. As MIB tossed the white stone into the ocean as an inside joke, could it be that there are much larger meanings here?
Is it possible that the black-white stone role, as personified by MIB and Jacob take on the ancient civilization role of condemnation/rejection vs. acquittal/acceptance? Are those who are currently with MIB no longer candidates and have been "judged" or rejected/condemned? This could fit in well with the images of Anubis and MIB that counter with Jacob's association with Horus. Those with Jacob on the beach have been acquitted (for example Ben) or have been accepted (Hurley/Jack). Thoughts?