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