I usually structure my Zend Framework projects like the image on the right. This comes almost straight from the ZF documentation for recommended project structures framework. I’ve been stressing using PHPunit more and more in my projects and endeavour to include tests for all my classes. When you are connected to a DB, it’s harder to test, but with the help of the Doctrine2 workflow, I think I’ve found a nice way to keep DB updates out of my Unit Tests.