dependencies between models, without using any ORM or DataMapper systems

[eluser]johnpeace[/eluser]
I would probably do it this way first:

"This first (knowing it isn’t elegant) is calling methods from one model to another,
for example: on a “many Documents per User” dependency, when deleting a User, the User_Model will directly call the delete method on the Document_Model, deleting any associated documents to it."

It's just simpler, easier to read and more straightforward this way.