There was an issue with 10.5 Server when working behind an authenticated proxy that caused a similar problem:
There are also issues - depending on which service(s) you're running that also caused similar issues. The SMB Service Log has been known to bloat itself to 100s of GBs given enough time. This can also apply to the Print log - assuming the Print Service is switched on?
On the Server itself, launch Terminal and issue this command:
sudo du -chxd 1 /
and provide the Server Administrator's password. There is no echo in Terminal so you won't see it being typed. Be patient as it will take some time to run depending on how much data you have and quantity of files.
Eventually it will give you a breakdown that will look something like this:
The above is an example only.
I'm guessing most of the space might be in /private/var/log? You can access UNIX sub-directories (which are always hidden) using either the command line or the "Go to folder" option in the Go Menu. It's quite safe to remove and delete old logs (as well as stale print jobs stuck in the cups folder - assuming you're running Print Services?) if you deem they serve no purpose?