I would see how your users actually use the site.
If you find a good separation of GWT applications (each user sticks to their small GWT application), then I don’t understand why you cannot separate them.
If, however, you find that your users are constantly switching from one application to another and impose the overhead of running another application, then you might want to consider one monolithic application. I would be inclined to this approach, unless, of course, you are doing very intensive applications. I doubt that browsers will have many problems with highly optimized JavaScript GWT.
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