Now the modules are more flexible than before. A module can hook menu, profile, and dashboard.
You can do more things in a Jcow v3 theme. Open the default theme source code, you could find how it works. Homepage content was written to the theme.
There two menu in Jcow v3: "Community menu" and "Personal menu".
Community menu contains the community links, like "browse people","public news",..
Personal menu contains links that only matter to the current user, like "my photos","my groups",..
Permissons is integrated with modules&menu. If you added a protected link in a new module, a corresponding form will be generated automatically in the permissions setting page, so that you can set who can access that page.