Speaking as a person with an undying hatred of (well, a mild annoyance with) the containers in general, or at least Tomcat in particular, I'd appeal for a balanced approach to this. It is vastly easier to debug a service using the embedded Jetty endpoint. You just run from Eclipse (or whatever) and there you are. No titanous struggle to get your stuff into the WEB-INF directory, no fighting with multiple incompatible debugging disciplines. And if your goal is a service tucked into some other application structure, well, there you are.
I agree that, sooner or later, most services will have to be transplanted into a container, but this is a process so annoying as to motivate the programmer to defer it to the last possible moment. Get all the service-side code working, and \then/, ahem, go to WAR with it.
