You may be plagued by this question often when you are starting to evaluate web service technologies in the Java EE space.
A good article that has take a decent stab at addressing this issue is:
http://www.ibm.com/developerworks/webservices/library/ws-tip-jaxwsrpc.html
In my honest opinion, you should choose JAX-WS because it brings you simplicity. EJB3 with JSR-181 type web services is the ultimate choice.
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