The Registry cleaner is for advance users. This I believe. You have to have an understanding of the registry and what it does before you do anything to it.
The registries primary function is to tell the applications where something is that it needs and the settings it needs to load.
That said when you run registry scanner it will show which registry entries will be removed or changed and you have a choice of which ones you want to delete.
Now with every windows update, application removal, application update, windows repair and any use of a security application such as virus scanners will alter the registry or leave things that are no longer used.
When an application is removed windows does not always remove the registry entries. This causes the size of the registry to increase and that causes the computer to slow down some.
Then you have entries that are added from updates. These updates add new registry entries but leave the old ones sometimes and this will cause flaky operation sometimes because the old entry is used and can not load the application correctly.
Below is a picture of what was returned from a scan of my registry as you can see it only returned one item. This is because I will run this at least once a week. This keeps the registry cleaned out. But that does not mean I will never have a problem with an application because of the registry. What I do if that happens is to do a uninstall of that application and then run registry scanner and clean registry before reinstalling the application.
This shows an issue Win7UI.exe. For some reason most likely an update removed it or moved Win7UI to a new location.
Now if that application can not open something that is needed using this registry entry then this registry entry is wrong and should be removed.
Removing this entry will not cause any problems that you don't already have. Another words if you already have a problem with an app this will not do anything to help with that app but it will remove the entry that if you reinstall the app might cause problems.
As to backing up the registry I do save the back up but not to reinstall it but to open and view it to see the difference in an old setting and a new one if I am having some problem. If I have a problem that I have to revert back to a previous time then I will use the the restore function built into windows.