I just recently went to Lostpedia and read about the whispers. I looked at them in the past and always kind of just thought that it was something to do with Psychics.
Now, after reading them again, I'm starting to think they're coming from beyond. It sounds like they're ghosts. Especially when Shannon dies and you hear them, they welcome her and someone says 'hi sis'. Maybe Nikki and Paulo will play a role later.