I know a lot of different things have been proposed about Jacob, so I thought Id throw my 2 cents in.  At this point, the theory is not completely 'fleshed out' as it were, just more of a 'What if" scenario, but here goes:

Jacob may be Lockes brother?  S1 Locke talks about playing the game 'Mousetrap' with his brother, so we know a brother exists.
We have also seen elements of time travel, with Des's visions of the future, and possibly real trip back in time.  So Jacob being Lockes brother makes a strange kind of sense.  Possibly Jacob was traveling, or a member of Dharma, got caught in the origianl 'incident', was transported back to the Black Rock era, and came back to find the island.  His ship (Black Rock) was caught in the volcanic activity in the past (tidal wave would explain how it is so far inland, as would the fact that that was the original beach, and the volcano expanded the island), and he is now trapped in a 'limbo' of sorts here.  Ben may have seen the resemblence to Locke, so might any of the others who have seen Jacob.  So now we know why the Others are so interested in John.  The 'Help Me' from Jacob to John would make more sense, he is asking his brother to help free him from this limbo trap that Ben is either keeping him in, is unwilling to help with, or unable to help with.  Ben, not wanting to see the source of his control compromised, does not want John to see Jacob, and once he does, wants to ensure that John doesnt free him, hence the shooting.  

Im sure the wonderful people here will help me to either point out the holes, and possible solutions, or shoot it so full of holes that it just dies off!

John was raised in foster homes, so I'm not sure that any of his "siblings" are biological but just other foster children. His mother doesn't seem to be overstocked in the maternal instinct department and Coop doesn't stay in one place for too long so who knows if he has other children. It's unlikely John has any full siblings and may not know of any half-siblings.

True, but if (as has been speculated elsewhere) Locke is a Hanso descendent, he would have to get those genes from one parent, so why not Cooper?  With all the connections on this show, its not out of the realm of possibility that Jacob and Locke are related.  

I'm not sure why it's been speculated that Locke is a Hanso?

Im not either, but I have read that in several places.  I think it has to do with the theory that Jacob is a Hanso, and that Locke is descended from them?

I haven't bought into that theory. It is just a dream without any basis in the show or the ARG. I'm also not convinced yet that Jacob is Hanso. Why give up the name Magnus? That is the type of name you'd name a condom after why would you lose it?

a CONDOM!  lmao!!  I agree ralf, I havent bought into all that yet either, but Im not ready to give up on the Jacob is related to or is Locke idea yet.  Need more holes!  (in the theory, not the condom!)

Ralf, I agree with you. Theorizing that Locke is a Hanso is just pulling two names from a hat. I can make up a theory that Sawyer is Ben's brother, but where would I get that from? It's just so random.

I think its more plausible to assume Locke and Ben have a connection to be honest, if we are trying to find a connection.

For example, we do not know for certain where Ben was when he was a small boy. Roger certainly seemed disgruntled to have him. For all we know, he may have been in some foster care and had a Locke connection. Plus they have mothers both named Emily.

But names get reused on this show so often.

If we start making connections based on names, does that mean Libby was married to Hurley's dad cuz they were both named David?

LOL. That would be an interesting twist, actually...