Which version of JBoss do you refer to? JBoss AS 4 has Jboss MQ installed by default. JBoss Messaging is the current active Messaging product supported by JBoss 4/5. HornetQ is the latest messaging project. It is much more powerful and been in active development. HornetQ 2.0.0.GA has just been released. If you are designing a new project, I'd suggest you try HornetQ.
Forgot to say, JBoss Messaging and HornetQ are enterprise level messaging products. I'm not sure about MQ series, but I think you can compare yourself if you know MQ series.
I don't know much about JBoss MQ. You can ask about it on JBoss MQ forum.