How did you end up in this situation? New HD? one day this all of a sudden happened?
Try to show the hidden folders: http://www.howtogeek.com/howto/windows-vista/show-hidden-files-and-folders-in-windows-vista/
Also try this application: http://windirstat.info/
. This app as an easy way to analyze the contents of your HDs. Much easier to find out what takes up space than Windows. This might help solve your problem, but if it doesn't, this program will help you in the future.