Recently, while installing CRM on a client’s server, we discovered a "broken" SQL Server installation. Enterprise Manager wouldn’t run, and certain SQL Services were no longer working. In order to clear this up, I tried to do an uninstall and reinstall of SQL Server. Unfortunately, during the uninstall, it errored out. So I was left with a SQL Server install that wouldn’t uninstall, and wouldn’t run. In trying to reinstall it, it would not allow an installation as the default instance.
Fortunately, Microsoft has a document on how to repair a disaster of this level. Take a looksee at http://support.microsoft.com/kb/290991 and follow the instructions very carefully. After doing all those things, you too can have a working SQL Server 2000 installation.