/
/core
/core/template
/core/database
/core/controllers
/core/validators
/core/components
/core/components/user
/core/components/menu
/core/exceptions
/docs
/modules/
/modules/modulex/
/modules/modulex/views/
/modules/modulex/controllers/
/modules/modules/models/
/data/
/data/images/
/data/css/
/cache
/libs
/libs/smarty
/libs/propel

Seperate folder (the webapp):
/index.php
/randomcrap(imagery and such)

I typically try to split off the webapplication from the framework so I have both in different locations. Reusability and such.