Q. I'm missing a lot of disk space on my Windows Server, how can I find what is using it?
A. I recently saw this problem. The challenge can be is if your user account does not have permission on the file which means normal commands to view folder size will not capture the size of the guilty data. The best tool I have found to track down large data is http://windirstat.info/index.html which seems to find data size even if you as the user don't have permission to view it. It will help highlight the folder containing the data. A common culprit is SQL Server which changes the permissions on its data files folder to remove inheritance and ACLs the folder for the per-service SID. This stops access even for administrators administrator access.
Additionally shadow copies can consume large amounts of space. This can be viewed using:
vssadmin list shadowstorage