Browse the filesystem and registry native using Total Commander to locate items hidden by Win32 rootkits.
Total Commander is a great file manager that offers an easy plugin structure for various browsers.
These plugins do allow you to browse the file system and the registry inside TC, with the small extra that it does so by using native Windows NT (2000, KP, Vista...) functions. This can come in useful if you're dealing with rootkits that hide some files from view from regular Win32 applications.