Smoke Monster
No, it's not really a smoke monster. Instead, mirror matter theory offers an explanation.
Foot proposes a way for the two types of matter to interact... "kinetic mixing" via the exchange of photons:
"If there is a photon-mirror photon transition force, then now an ordinary electron can actually interact with a mirror electron. ... The net effect of the transition force is to make mirror electrons interact slightly with ordinary electrons."
Let's spin this to imply that light (photons) will facilitate interaction between matter and mirror matter. This will be strongest when photons in our world are present (and overlapping with) the photons present on the island. But the moon is deep within the earth—rarely even approaching its surface.
What would produce light at that depth in the ocean (or underground in Africa)?
Answer: Bioluminescent sea creatures, mining equipment in African mines, and subs and little robots like the ones Naomi mentioned.
The point: The smoke is light from our world "kinetically mixing" with photons on the island. The smoke always takes the shape of clouds of light: faded at the edges and often drifting — just like what happens when a current pushes ocean debris through the light emitted from subs and deep sea robots.
This predicts the smoke should:
Always approximate the shape of light from a realistic source in the ocean or in a mine.
Only ever appear for about 2 minutes (so far this is true), as the moon needs to be brushing one of those locations (within reach of a light source) for this to work.
Only appear at some multiple of 144 minutes since the last time it appeared.
Be able to appear in multiple spots simultaneously if there are multiple light sources.
Respect the orientation and depth of the island.
Let's look at the position and orientation of the island at some moments when the smoke monster has appeared (this stuff and the remaining incidents are noted in the timeline above).
The timeline says about the time the pilot was yanked out of the ****pit, the island was exactly upside down at the bottom of the ocean at the Americas South location. Deep sea subs routinely go on scientific missions to the ocean floor in this region of the ocean and they all have hydraulic arms at their bow that could grab the pilot. So the arm grabs the pilot and then drops him when the moon moves away from the area (taking the ability to interact with the island with it).
Day 50, before noon. Eko is photographed while Charlie is in the tree. The island happens to be in exactly the same position as it was when the pilot was grabbed. So it makes sense that submersibles might show up again. Because the island is upside-down, a remotely operated vehicle (ROV) would be launched from the bow of a sub and then descend, breaking through the ground of the island.