So the nerd level of this post is slightly higher than normal, but I have recently been working on a couple of Windows Server 2008 R2 systems. The machines are running on VMWare ESX 3.5.
Randomly, and usually while browsing the Start Menu or Windows Explorer, the system would hang. It was still responsive to ping, but I could not access the system through VNC, Remote Desktop or the VMWare console.
I started searching for answers and came across this thread, which points to the VMWare SVGA II driver as the problem on Windows 7 and Windows Server 2008 R2.
The recommend doing a custom install of VMWare Tools to deslect that SVGA driver, but I found that disabling the driver in Device Manager was just as effective and faster.
So if you are having random lockups, freezes, hangs or stalls on Windows Server 2008 (or Windows 7) and you are running VMWare ESX, disable the SVGA II driver and you should be good to go.