Isn't it annoying how deleting a folder from your wwwroot$ doesn't automatically remove the corresponding website in IIS? You have to go into IIS and delete the website. If you're lazy like me, you probably have about a dozen left-over zombie websites waiting to be deleted (or eat some brains).
Well, there is a better way. Remember those hoary old FrontPage extensions? The Microsoft proprietary version of WebDAV? Well, they're still around. At some point in 2002 the FrontPage extensions were brought under the SharePoint umbrella. I still don't fully understand the nature of this relationship, but you may see it referred to by either name.
There's a handy Check Server Health page in the FrontPage Site Administration tool that lets you auto-repair all webs:
Select Repair and Detect for Verify existence of webs, then click OK. This removes all orphaned websites at once. Easy! One caveat: if you are running a real non-crippled IIS, the FrontPage/Sharepoint extensions will show up as another website on an alternate port, instead of as a subfolder.