Just some friendly advice - forget about using WM (Windows Messenger) for your application. Its not really 'free' if you plan to use any feature besides voice.

In SIP mode, IM (and I'll bet WB (whiteboard) has the similar issues)  expects a header that  contains a key generated  by  LCS.  I dont know of  anyone  who has managed to 'crack' this and use SER as an IM/WB proxy for WM for free.

If you must use WM, then LCS is your only real option for fully functioning system - and that will cost you per seat for Microsoft. They might have some education discounts or freebies but setup of what you want will still require someone to host it and/or consulting fees for setup. Any you will still have firewall issues unless all remote users have a uPnP router.

Another approach for you it to use the sipc system. It free for educational and research and I bet it work with SER (but haven't tried myself).

http://www1.cs.columbia.edu/~xiaotaow/sipc/

Mark