With the latest version of the XrmToolBox and the WebResourceManager plugin, there is now a new feature that displays a list of “unused” web resources. Well, it is in fact a list of web resource without any dependency. It does not mean that they are not used by other web resources, but it is a reduced list of web resources to analyze to check if they are still in used.
Then with the “Delete selected web resources” button, you can delete web resources you don’t need anymore.
Hope it will help you maintaining clean web resources list!