Although it is Groovy, not Java, I would advise you take a look at Griffon, which is a “Grails for Swing“.
It enforces a given structure (in terms of directories and patterns, MVC in particular) to all applications you build with it.
I think it can give you good ideas in general, although you would have to perform some little adaptation to Java.
Besides, please note that Griffon also supports Application building in Java, and it may also provide “archetypes” for that, so you could check that as well.