[eluser]Rolly1971[/eluser]
well not sure if this is correct 'best practice' in this case or not but this is my structure:
first off, for class files in the core folders of controllers, and views i primarily use folder based structure.
My Application requires a seperate members area to the rest of the site (eg: seperate from the front end).
Controllers/
--/admin <all controllers for administration are in here>
--/members <all controllers for members area in here>
welcome.php <this is a streamlines controller that handles all the front end pages which are dynamic>
views/
--/admin <contains all the admin themes each on has it's own root folder in here>
--/common <any view partial that is required by admin, members area, and front end>
--/members <themes for members area, can be overridden if desired and use front end theme>
--/themes <front end site themes>
----
Now modules are a bit of a different thing, file prefix 'tags' in modules to simplify the structure.
admin_ prefix is used for just that, members_, and public_
these tags are used in controllers and views.
models and library classes are a flat file structure, each class file is is given a meaning full name as to what it is for eg: forum_model, ect ...
but like i mentioned, is this 'best practice' ? probably not. But it works for what i am doing and makes sense to me for the most part.