I'm kind of nutty about keeping a clean system on my computers and I will always run CCleaner at least once a day, usually several times a day.... but that is just my preference as I do a lot of web looking and reading, so there is a lot of temp file for me to clean........ Most folks who can be classified as more "normal" than me....

.... would do quite well running it on a regular schedule, once or twice a week should be quite sufficient.... Folks that don't do a lot of web searching or looking at photos or listening to music files could get by doing it even less..... It really depends on how much activity you do with your computer.....
The program is recognized as extremely safe at so many different sites, or on tech blogs, that one really doesn't have much to worry about. And, as you found, it is much more efficient and thorough than the cleaner provided in the System Tools provided by M$...... I don't run the registry part that often, usually just after I uninstall programs .... for anyone nervous about doing that, I would recommend do the back up of the registry that it offers to do.... it just puts a small text file in your "My Docs" which you can double click on to have it reinstall itself in the registry....... I haven't backed up in more than 6 years of using the program, but again that is just my preference, and each user has to do what is right to them......
That's the fun of using these contraptions, we set them up and run them to suit our own needs which well can be entirely different than other users...... Kind of like adding things to our cars or our houses, making them suit our happiness..... Hope that gives you some reassurance with CCleaner, along with SpywareBlaster, I think they are the 2 most critical programs for us to have.......