One of Microsoft IIS 5.0 and 4.0's best features is the ability to store all registry parameters containing IIS's configuration in one file. IIS stores all changes to its configuration in the file %systemroot%\system32\inetsrv\metabase.bin. To create a backup of this file, start the Internet Services Manager (ISM), right-click the server you want to back up, and select Backup/Restore Configuration.
The primary use I've found for this feature is managing change control on production configurations. Adding the \%systemroot%\system32\inetsrv\metaback folder to my routine backup schedule and using the Backup/Restore Configuration utility to create a new metabase backup file after every configuration change gives me an accurate record of Web sites' evolution. In the event of corruption or other problems, I can easily restore all configuration changes. If a server fails, or if I need to roll back to a previous configuration, I can restore the .md file to restore all registry settings that control the virtual directories, default documents, and other server settings.
If you want to restore specific changes without altering changes to other sites, you can download the IIS MetaEdit 2.2 utility at http://download.microsoft.com/download/iis50/utility/5.0/nt45/en-us/mtaedt22.exe. This free utility lets you view and manipulate the metabase.bin file or any of your backups.