I've got a fresh out of the box PowerEdge T620 running Windows Server 2008 R2. There are two partitions, the C: drive with 39.9 GB and the 😧 drive with 793 GB. Windows is installed on C:. I haven't installed anything on the server.
Out of the 39.9 GB on the C: drive, only 2.62 GB is free. If I double click on C:, select all, and go to properties, it says the files only take up 16.5 GB. What else is using up space on the C: drive? The first thing I tried to do on this server was install .Net Framework 4.5.1, but it defaults to C: drive (which I don't think can be changed) and fails because there's not enough disk space.
How much RAM do you have installed? Don't forget the pagefile will consume roughly 1.5 times the amount of installed memory when there is sufficient space. I suspect you have between 12GB and 24GB of RAM installed.
Move the pagefile to your 😧 partition.
Delete D:, extend C: to a manageable size in Disk Management/diskpart, create new/smaller D:.
If you use a utility like TreeSize to view the used space on the disk, it will actually show you the pagefile size (or you can enable view of hidden and system files).