I use CCleaner more as a one-stop shop for uninstalling applications and managing start up and browser plugins than anything else. I do use the cleaning functionality every so often, but I do uncheck a lot of the features before I do. I don't need it to get rid of my internet history or list of recently used spreadsheets, but I do have it to remove some types of temporary files.
I think apps like this CAN begin to be counter-productive if they're used on a regular basis. Sort of similar to the "app killers" on Android phones, which just end up using more processor cycles and battery juice. CCleaner is pretty safe, but if you regularly have it to remove certain index files and such, your computer just has to spend time rebuilding those all the time. Similar to the "cookie" example given above.
For that reason, I regularly use some of its other features, but not so much the "cleaning" stuff.