I have been into this issue for a long time after installing Microsoft SQL Server 2005 in my PC. I had to create multiple server instances in my PC for different projects. But after using them I felt it was just a waste lying there and couldn't find a way to remove them. Interestingly the SQL Server Management Studio or the Enterprise Manager itself didn't have any option to do so.
A friend of mine recently showed this article of how to do it....
http://www.mydigitallife.info/2007/10/14/uninstall-and-remove-multiple-database-instances-of-microsoft-sql-server-2005/
