In our own project we have used JMS but not to communicate between two disparate systems but to get the asynchronous capability integrated to our application. What we do is push the message into a queue and get along with the rest of the business process. But from what i see this is not the correct way of achieving this. Of course at the end of the day we have achieved asynchronous behavior but not in the right way. A solution just came to light a few months back with the release of Spring 3. Spring 3 provided an implementation allowing asynchronous capability with the @Async annotation. I will not go into the details of this feature as it is very well explained here.
I have changed the previously JMS oriented code which mimicked the asynchronous capability and introduced Spring's Async implementation as i felt it was much cleaner and reduced all handling i needed to do with onMessage(),Connection Factory and the rest of the code needed to deal with JMS queues and topics.