Yes, if you have Windows 2000, XP, 2003 or Vista, Spybot-S&D does allow you to scan inactive Windows versions as well, including the registry of other installations!

To scan your system including installations on other partitions, right-click the link/icon you use to start Spybot-S&D, click on Properties, then on the tab shortcut and insert /allhives (separated by a space from the rest) in the box target. If you start Spybot-S&D through this link, it will automatically detect other installations, and scan their registries and files as well. From now on, that will happen every scan, so please delete the command /allhives if you do not want to scan several hives any longer.