An interesting feature of WebSphere MQ is support for WebServices. Using WebSphere MQ as a transport for web services is not a default choice... HTTP is the default mechanism for web services in many toolkits. Some advantages that WebSphere MQ offers are enhanced quality of services, asynchronous invocation, etc... Recently Axis 2 client support is introduced, so one can use standards like JAX-WS.
The documentation is available here: http://publib.boulder.ibm.com/infocenter/wmqv7/v7r0/topic/com.ibm.mq.csqzau.doc/ts10120_.htm . To start with SOAP/JMS its recommended to try this tutorial. The tutorial uses SI-Bus in WAS (not WMQ) as the transport, but gives a good introduction to get started with SOAP/JMS.
Here are some tips while trying out the samples in the MQ information center. Before creating the EJB and EAR projects, create the required queues in WebSphere MQ, activations specs etc in the WebSphere Application Server (WAS), else some failures are seen in the Rational Application Developer 7 (RAD). Also its recommended to update the Test environment and the RAD to the latest fix pack. To test the web service deployed in the WAS environment you can use the Universal Test Client.
Some interesting tools that help in developing and deploying web services are also provided. One of them being amqwdeployWMQService which can be used to create WSDL files and prepares a service class for use as a Web Service. So you can start with simple Java file having a function that you want to expose and Web Service and run this tool to understand how the WSDL files are generated.
Also observe URI patterns of SOAP/JMS request... this is difference that applications need to adopt if they were previously invoking a HTTP based web service. The URI pattern for SOAP/JMS specifies the queue name and the JNDI connection factory. If using "com.ibm.mq.jms.Nojndi" as the initial context in the URI string as described here, then ensure that com.ibm.mq.jms.Nojndi.jar in the Java\lib directory of WebSphere MQ installation is added to the classpath.