It just hit me that the cave with the names on the wall could be MIBs hang out and not Jacob's. As we have seen, Jacob dwelt in the foot of the statue. Why would he write all the names on a wall in a cave when he could write them on the wall in his home?
Maybe the cave is where MIB lived (when he was in human form). He is conning Sawyer to believe Jacob wrote his name on the wall when really it was MIB himself.
The counter-evidence to this theory would be Flocke throwing the stones. If it was his cave, then why would he react so negatively to his own belongings? My 2nd thought is that maybe MIB and Jacob wrote these names together or at least used to hang out in the cave together and plan out whatever it is they were planning (maybe when they were boys).
Also, I am getting the vibe that Jacob and MIB/Flocke/Smoke Monster are related. They are either brothers or were best friends. When Flocke saw the boy he seemed haunted by something he had done and seemed a little remorseful.
Jacob and MIB definitely give me the impression of Jacob and Esau from Scripture. In the Biblical story, Jacob conned his brother Esau and stole his birthright (which was also prophesied...aka it was his destiny). In the same way, Jacob from lost seems to persuade people to accomplish his own ends. Jacob has always seemed calm and in control while MIB/Flocke has seemed resentful and angry. In the Bible, Esau resents his brother and even threatens to kill him (the same way MIB threatens to kill Jacob). I know many people have come up with this theory before me, but it seems like it is being reinforced.