+1 Though question!
There is an answer to this question here (still on stack overflow) when using IIS. So I guess it is possible on a servlet container to fool the client into presenting some kind of signed token as proof of authentication. Then I guess you will need some windows magic to validate the thing.
Is there any "Integrated Windows Authentication" specification somewhere?. Did anybody implemented this? JCIFS, Samba?.
I would use tcpmon to see the interaction between the browser and a IIS if the recipe given above works. I suspect It is fairly complicated though. If there is not some crypto involved I would be very disappointed.
Tomcat has already support for LDAP authentication sources (see here). Maybe extending this and add a custom Realm implementation.