Hi,
you would have to check using Windows Explorer on your server, which files are there listed as system. (This is usually all stuff on the disks, which is not stored in folders used by Windows Home Server by default for backups and shared folders.)
Backup folder: D:\folders\{00008086-058D-4C89-AB57-A7F909A47AB4} (and on other drives under C:\fs)
Shared folders: D:\DE\shares (DE folder hidden, also to be found on other drives)
These two are folders, which you should not touch.
In d:\folders\{1618D36B-F4E7-4360-B070-A32070519DC9} you could find lots of lost stuff, which takes up space on the system pie - the files in this folder you can remove after ensuring that you have a good copy of it.
Best greetings from Germany
Olaf