I'm just getting started as a beta tester for ArcGIS Online for Organizations, and I also wonder about how to organize lots of maps. It seems that Folders only exist for My Content, and that capability only helps to keep maps organized for yourself. In order to organize maps for your organization's users, it seems the only recourse is to create Groups, which I guess can be thought of as a kind of 'Folder', but as with My Content Folders, there is only one level (ie no groups inside groups).