Not read the whole thread so apologies if this theory has cropped up before, but I think I know what the smoke monster is. I'm guessing its a manifestation of the island's power meant for protecting the island.
We've already had some strong hints that the smoke monster has been around before the MIB falls into the cave. Some of the Egyptian stuff we have seen indicate they worshiped the smoke monster in some way.
Also, in Across the Sea there are several indications that the mother is in fact the smoke monster.
1. She kills a whole load of people
2. She fills up a massive hole in the ground with dirt in a short space of time.
3. She warns Jacob not to go into the light because it would be 'a fate worse than death'
4. She thanks the MIB when he kills her, implying she was suffering said 'fate worse than death'
I think this indicates pretty strongly that whoever becomes 'protector' of the island is supposed to enter the light and become the smoke monster and gain its abilities in order to better protect the island. It is essentially a weapon left behind by the whoever created the island, so its appearance and all the weird noises it makes are a result of intelligent (technologically advanced?) design rather than anything random. The ritual that Jacob goes through is only one part of the puzzle. Unfortunately his mother warns him away from going into the light, probably because she herself regrets doing so. The skeletons in the cave also indicate others have entered the light and are probably the remains of previous protectors who shed their physical bodies in order to become the smoke monster and protect the island.
However in this instance Jacob chucks the MIB down the cave instead of going down himself which results in the MIB gaining the island's 'weapon' instead of Jacob. Fortunately Jacob still has his powers over the island and the ability to set rules, so he puts some rules in place that prevent the MIB from ever being able to leave the island and unleash it's power upon the human race, which he would probably do since he has already told Jacob that he finds humans to be 'bad'. Jacob also acknowledges that the MIB may one day find a loophole in the rules and be able to leave the island, so he brings people to the island in the hope that he can change the MIB's opinion of the human race and if, one day, god forbid, the MIB does escape, he will be less inclined to decimate us. The MIB, in turn, tries to prove to Jacob that all human beings are bad, in the hope that one day Jacob will agree and stop giving a shit about humans and let the MIB leave the island to do whatever he wants.
I find it interesting that all the conflict in the show boils down to the upbringing of Jacob and the MIB. If the islands protector was a regular person with some life experience and hadn't been raised in seclusion with weird views of the rest of the species none of this conflict would have happened. Which is why I believe Hurley will make a good protector
