One program you may want to look into is JV16 Power tools made by Macecraft Software: http://www.jv16.org/
It makes backups of deleted items so you can always get back to before you started. I totally trust this software and have used it for years, and it does a lot more then just registry cleaning.
There's also an older free version floating around here: http://www.321download.com/LastFreeware/
But I would recommend the commercial version, you know "support your local programmer".