The black smoke is some kind of force that could be animal or man-made. Season 2 is when we began to see it, with the same grinding noises we heard when the monster had appeared in the past.
When Eko wouldn't confess to Yemi, the black smoke killed Eko (Ep: 3x5, The Cost of Living).
In a later episode, the smoke chases Juliet and Kate and is stopped by the sonic fence, which it doesn't seem to be able to go over (Ep: 3x15, Left Behind).
Later, it does get into the Others' compound, presumbably because Alex had turned off the sonic fence. After Ben goes into his secret room, the black smoke appears like a long snake and attacks Keamy's men (Ep: 4x9, The Shape of Things to Come).
Man in Locke disappears from the statue and the smoke monster comes out and kills Bram and his men. Man in Locke reappears and tells Ben, I'm sorry you had to see me that way." (Ep: 6x1, LA X)
In episode 6x15, Across the Sea, we go back in time to see Jacob and Man in Black growing up. As adults, Jacob beats Man in Black after Man in Black kills Mother. Man in Black hits his head on a rock and floats face down into the light cave and the black smoke comes charging out.