Alasdair Wilkins in io9:
We're still waiting on analyses of the dead birds that will solve the mystery, but there are already several theories to account for the deaths. So far all we know for sure is that the Arkansas birds showed signs of blunt-force trauma, although it's possible that was just caused by slamming into the ground.
Weather could be the culprit. High-altitude hail or lightning might have hit the birds, which caused them to fall from the sky. Arkansas Game and Fish Commission ornithologist Karen Rowe says a severe weather system did move through Arkansas on New Year's Eve, so it's not impossible. The only problem is the birds don't seem to have any of the telltale bruises or injuries that a weather-related explanation would cause.
Thankfully, we can probably rule out disease and toxins. Arkansas experts say a disease would take down a lot more than just one isolated flock – and no, the second group of dead birds in Louisiana isn't enough to make disease seem like a viable possibility. The same thinking goes for poisoning – if that were the case, birds would be falling all over Arkansas, and that just isn't the case. The Arkansas Department of Environmental Quality tested the area for any air toxins, but the skies are officially clean.
One thing to remember is what day and time the incident occurred: near midnight on New Year's Eve.