From Lostpedia: Whispers from an unknown source frequently appear when characters are in peril, when the Others are near, or during other moments of tension. These are not random noises, but rather actual speech, and can be decoded using audio software.
Most of the whispers are directly related with the survivors, and who ever whispers seems extremely reluctant to interact with the person that notices the whispers. Also, there are names of main characters mentionned (Sawyer, Shannon, Ana Lucia etc.). Finally, the whispers seem to be connected with crucial events on the island. All this makes me think: What if somehow the consciousness of the people on the island, especially of the ones that were at the Swan Station during the "incident" didn't exactly time-travel (like Desmond', Minkowski, Theresa, for instance), but were trapped in the time-loop in which the island is? What would that mean for those that "are coming", according to Jacob?