I have a new article on developerWorks, "Running a standalone Java application on WebSphere MQ V6.0."
It's an update of my previous article, "Developing a standalone Java application for WebSphere MQ," which was written for WMQ 5.3. For this version, I have as co-authors T. Rob Wyatt and Kulvir Singh Bhogal; so to the extent this article is better than the first one, give them the credit.
I hope you'll find it useful for learning about JMS and JNDI and how they can be used in Java SE (not just Java EE), as well as how to admin and configure WMQ.
Running a standalone Java application on WebSphere MQ V6.0