for example, if my WINDOWS or Documents and Settings folder were on a different partition, would CCleaner still detect them?
I believe that it only scans the drive that it is installed on.
edit: posted in suggestions section
A great feature in CCleaner is under OPTIONS->CUSTOM. There you can add individual files or whole folders to be cleaned. Plus under the "Cleaner Windows" tab, the Custom option can be selected on or off,via the check box,at each run.