This is base on my app-engine-starter but works outside google app engine. Also note that I changed main.py to wsgi.py and made the application variable so it works with appfog.
Summary of things::
lib/ - will hold your custom libraries, thirdparty libraries usually just go on root folder
models/ - all your endpoint messages and datastore models here
services/ - web services like cloud endpoints or your custom jsonrpc services
static/ - js/css/images and all other static files (templates for js html)
templates/ - jinja2 templates goes here
web/ - webpage handlers
tests/ - unit testing tests goes here
config.py - any configurable things on your project to easily edit later when you adjust things
routes.py - all your routing needs for your url mapping to webpage handlers
Note that this is just a guideline, following it will just make life things easier when your app grows to hundreds of files.