My two cents... This may eliminate some options...
I installed iOS 4.2 on my iTouch last night. I went to set up my link with Ubuntu on my main machine and got the message "Charging is not supported with this accessory" when I plugged into my USB port. After reading this post I tried another USB cable, and a reboot, but neither worked.
I tried plugging my iTouch into a USB charging device USING THE SAME TWO CABLES I USED WITH MY PC, and the iTouch behaved normally.
I tried plugging it into a Windows XP laptop and it behaved normally. I tried plugging it into another Ubuntu computer, and it behaved normally, although this computer is running a slightly different version of Ubuntu.
My iTouch is configured in a standard fashion.
I am concluding that the problem is not the cables, and it is not the connector at the base of my iTouch.
My suspicion is that one of my computers is running at a slightly different USB voltage than the others, and that this difference is somehow triggering a reaction from my new iOS 4.2 installation.