<p>What is the functional equivalent of <a href="http://msdn.microsoft.com/en-us/netframework/aa663324.aspx" rel="noreferrer">Windows Communication Foundation</a> in Java 6?</p>

I don't know what all WCF contains, but
JAX-WS
(and its reference implementation
Metro
) might be a good starting point.
Some of the other
technologies in J2EE
may apply as well.