Have been thinking further about this, and although a portal style may be appropriate (and possibly should be an option available to users), I quite like the idea of creating an environment in which 'applications' are available to a user based on their role. The range of applications are not necessarily important at the moment, as they will probably grow over time, but in terms of web UI style this seems to fit the 'desktop' style. Some examples are:
http://www.gwtwindowmanager.org/ (although is probably not as mature).
However I am sure other libraries can be used to create the same style.
I have to say that the ext-GWT's desktop example very shinny, but because of the license issue, I don't think it is an ideal option.
I think we can start to use the smartGWT as our alternative library as a start point, either choose portal style, or maybe we can use some of their widget to create a desktop style like EXT one.