Amazon and Roku seem to make it hard to delete a Roku or other device from your Amazon account and most people say to go to the My Digital library and remove the device. However at time of writing (March 2012) this advice is incorrect.
Instead sign into your amazon account and then go to https://www.amazon.com/gp/video/ontv/pin
You will have your roku or other device listed, select delete and then confirm the deletion. Seconds later you will be able to register your roku with Amazon again. Of course if you don’t have access to the original Amazon account then you will need to factory reset the Roku first.