Insufficient USB power
This has been problem plaguing USB hubs and USB devices far before the Pi arrived. I have a number of computers backing up to portable/bus powered USB hard-disks - and after a few months of use a lot of them start to conk out in the middle of a multi-hour data transfer. The solution for me was a Targus USB 2.0 4 port desktop hub. This particular model (you can find it on Amazon - not sure if allowed to post links to products here) has two out of the 4 ports which provide 1 full Amp of power. This might be outside of the USB spec (500mAh) - but it certainly gets around the problem that some devices (specially bus powered portable hard-drives) need just slightly more power than the spec allows for - specially as they get a bit older and during prolonged data transfer sessions. No more problems for over a 1.5 years now and about 15 usb hard-disks and 4-5 hubs involved.