Basically, the differences are as follows: JBossAS 4.0.x is certified for J2EE 1.4. JBossAS 4.2.x adds EJB3 and JAX-WS support. JBossAS 5.0 will be fully Java EE 5 certified.
In addition, 5.0 is a major move to being based on a microkernel, rather than on the JMX kernel.
As far as JBoss Portal goes, the Portal team qualifies their product only on the latest GA version of JBossAS. This means that the latest Portal (2.6.5) will run only on JBossAS 4.2.2. Not until JBossAS 5.0.0.GA comeso ut will the Portal team attempt to qualify the portal on 5.0.