I using the Windows Indexing Service for the search on of my web sites because most of the content is in flat files. I haven't touched the configuration for years and it works fine (even though the search results are not always what you would expect).
Recently I added two new subdirectories to the site, a normal one and one virtual directory for DasBlog.
I didn't really thing about at the time but realized later that I don't want any of the two new directories to show up in my search results as they are separate sub sites.
For a normal directory, you have to go into Indexing Service node of the Computer Management MMC and find your web site. Add a new directory and set the property to 'Include in Catalog' to No. In the same list
is also an entry for the new virtual directory but there is no delete feature as there is on
directories that you created yourself. Switch to IIS manager and look at the 'Virtual Directory' tab of the properties for the virtual directory. I unticked 'Index this resource' but they directory didn't disappear in Indexing Service. When I created the new virtual directory it inherited the 'Index this resource' property from its parent site and the Indexing directory was created. Changing the property doesn't remove the directory, surely a bug.
How to fix this? I exported the settings for the virtual directory into an XML file, deleted it and then created a new one from that exported file. The indexing service directory is gone.

This was on a 2003 Server, but should be similar on Windows 2000.