Are your servers in a different VLAN than your user base?
If so, there must be a layer 3 interface that routes traffic from the server VLAN to the user VLAN(s). It's that interface or subinterface whose traffic load your would need to measure. A simple performance monitoring tool such as MRTG can handle that task easily.
If not, you will be moving them eventually so why not just administratively separte them into a different VLAN before physically moving them? If you assigned IP addresses in a well-thought out manner, you might not even have to make any changes on any servers or clients, just a new L2 domain (VLAN) with associated L3 (routing) interfaces on your router or routing switch which you can then monitor as above.
If for some reason they are all mixed in with user VLANs, you have a much more complex task at hand and would need to monitor many individual interfaces (could still use MRTG), but you would have to somehow factor out any server-server communications - not easily done if they are within a given VLAN unless one resorts to packet analysis type tools - probes, sniffers, etc. - and that tool set doesn't scale well to considering 100 servers at once.