I'm sorry that you are having this problem. SQL Compare/Data Compare has been known to leave some temp files but on this scale I'd check first that the commands aren't aborting or failing before the temporary files can be disposed. That could potentially leave entire tables of data behind in the temp folder.
In the meantime, Windows Disk Cleanup is the best tool to put the disk right.
I believe in order to get that on Windows 2008, you have to add the "Desktop experience" feature.