Yes , there are both open source and commercial MOM software available. Personally I'd use an external broker instead of relying upon any built-in appserver JMS broker - it is easier to experiment alternative brokers, change providers, setup clustering nd so on.
I used to run ActiveMQ as message broker to send notification to clients and to
exchange messages among different services/applications (both written in
Java an .NET framework) and I feel comfortable with it, but I am pretty sure that alternative products are valid too. Have a look at HornetQ for example.