I'm still fairly new to laravel but I think it all comes down to project size and personal preference. I've tried organizing in sub folders, workbench packages, custom modules, and some of the module packages.

What I'm doing now on my newest project which I'm really enjoying is using creolab/modules package for app specific stuff and workbench packages for any generic stuff that I want to keep more easily reusable and to share with the community later.

Checkout the fusion invoice 2 source. I think that's a great reference that will help you understand that you are not at all limited by the default structure of laravel.

Hope this helps :)

Thanks guys, this was really helpful :)