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, and add /allhives to the command line (separated by a space from the rest). If you now start Spybot-S&D through this link, it will automatically detect other installations, and scan theirs registries and files as well.