What changes were made to the registry? Generally you don’t want to make any changes to the regestry of a production system without knowing exactly what you are changing. Applications which “clean” the registry can often make things way worse than they were before.
If the application made a backup of the changes which were made you will want to restore those changes and reboot the server. If the application removed part of the SQL Server registry keys who knows what else it removed.
If there is nobackup of the changes which were made then you will want to do a repair of the install of SQL Server. I beleive that if you drop in the CD/DVD you can run the installer and do a repair of the current install. After the install you will need to patch the server again to the same level which you are currently patched to. If this doesn’t help you will probably need to uninstall and reinstall SQL Server, and restore the master database. If you don’t have a backup of the master database you will need to attach your user database, then recreate all your logins. If you have a backup of the msdb database you will need to restore this to get back your jobs. If not you’ll need to manually recreate them.