Yet another idea on Colony Collapse Disorder in this article. An email list of 1000 organic bee growers have not reported any CCD related problems with their colonies. Also mentioned is:
“The problem with the big commercial guys is that they put pesticides in their hives to fumigate for varroa mites, and they feed antibiotics to the bees. They also haul the hives by truck all over the place to make more money with pollination services, which stresses the colonies.”
This article also goes on to explain that commercial bees are encouraged to grow large by providing them with oversized foundation cells, the cells bee keepers provide their bees when starting their colonies. This results in bees that are more susceptible to the varroa mites as well as possibly other problems.
It seems to me this might be a somewhat simplistic assement of CCD, but it may explain an important part of the problem.
The Bush Bees site has a lot of general information about bee keeping.