What is the difference between using JMS/Messaging Middleware versus Web services using JAXM? Which of them is more reliable?
A JAXM provider is not obliged to implement guaranteed delivery. That's optional and left up to the vendor. The JMS specification, on the other hand, explicitly deals with delivery guarantees, acknowledgement modes, priorities, queueing, etc. All of these are features you typically need when developing enterprise class applications.
Hence if reliability and throughput are important, then its probably fair to say that a JMS provider is the better choice. Also note that it's not an "either or" choice you are facing. Most of the JMS providers support SOAP in one way or the other (by transporting SOAP envelopes over JMS, or by implementing a JMS/SOAP Gateway). So you can actually combine the flexibility of SOAP with the reliability/scalability of JMS.
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