Patrick,
Funny you bring this up as this past weekend I was actually experimenting with moving everything into an application layout component. But I couldn't figure out how to handle a 3 column layout with 2 sidebar columns on the left or right. Maybe I could make that a choice in the Layout Document or something?
I think I will start investigating this a little more as the Dojo Border Layout is starting to get on my nerves a little bit (all the scroll bars everywhere) and the main reason I used it was the ease at which you could come up with complex layouts and everything would just fit to the page.