Core A, Runckel C, Ivers J, Quock C, Siapno T, et al. (2012) A New Threat to Honey Bees, the Parasitic Phorid Fly Apocephalus borealis. PLoS ONE 7(1): e29639. doi:10.1371/journal.pone.0029639
Yet another possible theory to CCD, one that NEEDS TESTING has come up as a possible cause of CCD. A parasitic fly, Apocephalus borealis, which typically uses bumblebees as hosts has been found to also use Honeybees as well. Their life cycles seem to overlap with that of CCD epidemics. Basically the fly injects eggs into the abdomen of the host and a few days later, I read, about 13 new flies burst out of the bee. While infected the host bee will continue flying at night in a daze, thus they don't return to the hive hive.
So there's lots of correlation here. The next step will be to find out how far spread these flies are and whether their populations are great enough to decimate whole fields of hives within their life cycle for the effected areas.