EXACTLY Who and What the Mysterious Boy Is by UnknownOther

Theories have been posted on this, but I know for a fact this is correct, and you won't have anything to prove me wrong.

In "The Substitute", MIB is talking to Richard when he declines to go with him, at which point he sees the blond boy, which both startles and puzzles him.

The blond boy in real life was MIB's son (and if not his son it's someone very close to him, who at a young age, was killed as a result of MIB's actions).

Richard doesn't see him which lead's MIB to believe this is an apparition of his dead boy, who is there specifically to remind him of the pain he's caused.

Later, with Sawyer, he appears again, this time with no blood on his hands, and this time Sawyer can see him. At that point, MIB realizes who this actually is: Jacob.

This explains why he chases after, and shows anger, not shock as he did earlier. Jacob, in the form of MIB's son, reminds him of the rule not to kill/claim any of his candidates against their free will, and the consequences of breaking those rules.

Losties who have seen dead people on the island (NOT as Smokey in their form) have been specifically from their own past, not anyone else's, and no one else has been able to see them. Example: Christian in the suit he was wearing when he came to the island. He is seen by Jack and Jack alone.

But losties who see visions not of their own past, are witnessing either Jacob or MIB, who are using those forms to manipulate or push them into doing something under their own free will. Example: Christian in the cabin telling Locke to move the island.

Sometimes, a combination of the two can occur, ex. Yemi, where the dead body appears to the person they are directly correlated in the form of Jacob or MIB.

The entire "game" is played by having the "pieces" move themselves using their own free will. While Jacob "pushes" his players towards an action, MIB manipulates them.

Jacob appearing in the form of MIB's dead son is simply a way to remind him of what happens when you break the rules.