Are the systems in question stand-alone systems or do they authenticate with a server (perhaps via LDAP)?
Unless they are authenticated via a server I don't see how any server-side app could use the local machine's authentication without including a client side application.
This is just musing, but it could technically be done via mac address or something, but that has some gaping security holes in and of itself.
If the Windows systems use Active Directory to maintain login ids for use in an NT domain, then you will want to use LDAP for login. Here are some reference:
LDAP login module info: http://docs.jboss.com/jbossas/guides/j2eeguide/r2/en/html_single/#ch8.ldaplogin.sect
LDAP with Portal: http://wiki.jboss.org/wiki/Wiki.jsp?page=UsingAnLDAPSourceForPortalAuthentication
And a discussion on LDAP and portals: http://www.jboss.com/index.html?module=bb&op=viewtopic&p=4051256
By the way, if you search the JBoss Portal forum for the term "LDAP" you will find several discussions.