I use Wise Registry Cleaner from time to time. It's conservative, and does proper backups. It doesn't mess my working system up, and usually perks up the performance a little (the first time I used it it made a substantial difference).
I do install, uninstall and generally "mess about" with my system a fair bit. I can't guarantee it will not mess up your system - but, as I said it does do backups.
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