Disk Cleanup has a lot of options when its opened from the command prompt

Click start --> Run and type in cmd type in chkdsk.exe plus one of the following switches. In the command prompt you will type in something like chkdsk.exe /X to run the desired operation.

/C Will skip the checking of cycles within the folder structure to do a much faster run of chkdsk
/I performs a not so thorough check of index entries, also making a faster run of chkdsk
/L[:size:] allows you to designate the size of the log file.
/X dismounts the drive before scanning. This is the most thorough scan available.

Cool, thanks. So chkdsk.exe /X will make you restart the computer and do that thorough scan in DOS mode?

No! dismounting means that it'll disallow all io activity to that particular drive ... and if the drive cannot be dismounted then it'll ask to run disk cleanup on next boot or not.