My favorite theory about last night's awesome revalations relates to the first scene with Jacob and Otherman. The idea is that the ship they see offshore is the Black Rock, and that Richard Alpert is on board. One of the biggest mysteries yet to be revealed is Richard Alpert's true identity, and why he does not age. I beleive it has something to do with what happens when that ship (possibly the Black rock with him on it) hits the shore. I think that Richard was a part of something between Jacob and Otherman, and through whatever events that transpired, was given the blessing/curse that he would never age.
This first scene is a key link to the entire story line of the series. Knowing that Jacob has an arch nemesis is no real shock, and I actually find it surprising that no one thought of that before. Every great character needs an opposite one to motivate them to do things. Even the great Jacob.