I have used ccleaner for some time and love the program. I have foudn recently that there is a windows folder that is not getting cleaned. The folder is "C:\WINDOWS\SoftwareDistribution\Download" this folder holds all the windows update downloads. In each of my system I have foudn over 500 MB for files in this folder. Checking around the internet it seems like cleaning this file is a good idea. I tried deleting all the files in this folder and then ran windows update again with no problems.
This might be a good folder to add to the list of folders to have ccleaner suggest for "cleaning".