Yeah thats been the problem since day 1. Every application thinks its settings are so globally important as to warrant placing them in the registry rather than a local settings file. Very few things are of such importance. Font settings, primary language, physical location fo the users MyDocuments folder, but certainly not all teh crap that most applications put in there, and magically dont remove when they uninstall.
I spent an hour and a half helping a friend manually clean his registry over a VNC connection last night, you woudln''t believe some fo the crap these applications put in there, and leave behind. ........ like the companies web address...
My personal viewpoint is that unless its something that some other piece of software THAT ISN"T MADE BY YOUR COMPANY will need to know, it doesn't belong in the registry.