Cleaning those redundant files and uninstalling unwanted applications is a real head ache. We realize the importance of space only when there is a need to save some important files from a CD or DVD.
As usual you have a lot of choices for this purpose, but rather than user friendly it is best to go with system friendly.
If you find something is wrong with one of your drives, then give a error check, with both the options selected.
When there is urgent need of few MB space just try deleting the temporary data in the system drive.
Like going green, just go system.