I believe that all throughout the show, we may have been witnessing two different smoke monsters. One is Jacob, the other is MIB.
The one that Locke encounters early in season one and describes what he saw when he looked into the eye of the island as "beautiful", I believe was Jacob. The one that encountered Eko on his journey to the beech-craft was also Jacob. Jacob has been looking for someone with a spiritual connection to the island to help him. I also think this is why they were each killed... but they were killed by MIB. Sure, Locke was not directly killed by MIB but he was sure set up by him. MIB saw these two as threats and allies to Jacob and took measures into his own hands.
I am unusure about Jacob's cabin. I think it was used by Jacob but he didn't live there. It's ability to move would make it an ideal place to leave his lists and instructions for Richard, to save him walking out to the Statue every time. But then again, was it really Jacob giving the lists? How do we know that MIB hasn't had a hand in this?
MIB's negative view on people makes me believe that his version of the smoke monster is the violent, murdering one. If Jacob really does represent free will, this would explain his "observation only" approach as he scans Locke, Eko, Kate and Juliet. On a side note, isn't it odd that Kate is the only one to have been scanned by the smoke monster that hasn't died... can MIB somehow use Jacob's scans to manifest himself as people close to the victims? Eko's brother Yemi, Jack's dad Christian?
Anyway, I know my theory has sort of branched off in different directions, I figure it might as well branch off once more. The "Cerberus Vents", the holes that the smoke monster appears out of and where it tried to pull Locke into... I believe we'll be heading down there this season and we'll learn what the smoke monster actually is.
And when it appears and flees, has anyone else noticed how it's usually consisted of three streams of smoke? Just something to think about.
Let me know what you think, don't hold back on the criticism either haha.