There's a lot of CCleaner paranoia here. Without exaggeration, over the many years I have known about, installed and run CCleaner, I have run CCleaner at least 10,000 times, the registry cleaner probably 3,000 times. In fact, I have a Windows scheduled task that runs CCleaner every hour (after 10 minutes of no activity) on my main workstation. I have every setting checked on both tabs, Windows & Applications, with the exception of Wipe Free Space. I have never had a problem on my workstation or any of my clients.
Additionally, of the thousands of times I've run the Registry Cleaner in CCleaner only once did I have a problem. After I ran it, Windows (ME, I believe) would no longer run. BUT, I knew before I ran the registry cleaner the OS had serious registry issues so it came as no surprise when Windows would not start.
In my opinion, backing up your registry each time before running the CCleaner registry cleaner is a waste of time and space.
CCleaner is an excellent, extraordinarily safe and efficient utility way of cleaning up a computer.