JBoss Serialization is used on EJB3, and could be used on Remoting if you configure it so.
Java Serialization still used on the Application Server in several places.
Another question is that whether the JBoss Serialization is used in JBoss AS 4.0.5 (or above) to serialize JNDI binding objects?
No.. just regular Object*Stream over RMI. (I believe it is part of the JNDI spec)