I read about this just a few minutes ago. Some theories I've heard: Virus, fireworks, lightning, aliens, and my favorite, 2012 is one year away so bad stuff is happening.
Oh; some people have been saying that it's viral marketing for a new The Birds movie; someone said a friend of his (of course) worked on it, and said they collected birds that died naturally and dumped them out of planes, then had actors in hazmat suits pick them up.
I think that's bullshit; PETA would throw an immediate bitchfit and sue them to Hell and back, and it seems like it'd be a pretty dangerous thing to do, with bacteria and whatnot.