..genetically modified crops.

Certain radically genetically modified crops pollen might act as a slow poison and the bees abandon the colony and go off to find a new colony or die somewhere.

Why?

The forced modification or accelerated gene-gun technique used to create certain crops may create pollen that screws up bees' royal jelly. If I recall my bee studies, each new bee is fed royal jelly for several days and then pollen and honey. Royal jelly is made in the bees' heads and is a glandular secretion. If the pollen is not what they are accustomed to, it may very well create glandular problems, which then screws up the royal jelly and snowballs through the colony, acting as a disease magnet. Their queen then can't serve her purpose and they can't create a new one with bad royal jelly, so they get all flustered and abandon the colony leaving only a few loyal attendants to the queen behind.

When they mix fish genes with plant genes and create other very "unnatural" combinations of genes, you start playing "god" with nature and you learn that quick fixes often create new, entirely unforeseen - and possibly devastating - problems.

Granted, this is just a WAG. But it would be very interesting to map the various colony collapses with any genetically modified nearby crops and match up dates when those crops were planted.