The Add/Remove programs feature in the Registry Manager is quite identical to the one with Windows, it uses the same uninstallation routines to remove the application.
However, the Software Manager in jv16 PowerTools 2005 allows you to remove left-over entries of software not included in the Windows Add/remove programs list.
And it gets better with jv16 PowerTools 2006 - the Software Manager is highly improved in a way it can uninstall many applications, even those not listed in the Add/Remove list.