Other ways to approach this from 2005+; You could use the article from the SQL team at http://blogs.msdn.com/b/sqltips/archive/2005/08/19/sqlregsettings.aspx to use CLR to both read and write to the registry checking the entries before writing. Or, you can use the undocumented stored procedures like master..xp_regread and master..xp_regwrite to change the registry.

Overall, if there are company wide flags that you need to implement, this is a quick way to do them, good article.