I have a theory that the mysterious boy will end up aiding the rest of the Losties in defeating the Man in Black. He seems to have some control over the Man in Black. When he told the Man in Black that he couldn't kill Sawyer, the Man in Black got really angry and exclaimed at the boy "Don't tell me what I can't do." Then when he was seen again by Desmond, The Man in Black told him to just ignore him. I think he is either a younger version of Jacob or maybe he is Jacob's son that has died.