On the Zend Developer Zone there's a recent post from Ralph Schindler talking about an update that's been made to the Zend Framework to improve generated testing stubs for Zend_Tool generated projects starting in ZF versions 1.111.4.

At the time of Zend_Tool's initial release, the standard application structure you are familiar with today was just being released as well with Zend_Application. In addition, the testing controllers from this newly standardized application layer, were too, in their infancy. [...] Recently, while Sebastian Bergmann was working on his pet project php-project-wizard, he noticed a few inconsistencies with the stubs that Zend_Tool was generating and decided to send us some recommendations on how to best leverage PHPUnit 3.4+ to test our application's assets.

He walks you through a newly generated project and shows (complete with screenshots) some of the updates that have been made like the new single bootstrap.php file, an updated phpunit.xml, a sample IndexController test and a bit of detail on what the generated tests actually look like.