As Ligaya Turmelle discovered when trying to work with the Zend Framework in a subdirectory, it doesn't want to play nice. After poking around a bit, though, she discovered a solution in the Zend_Controller_RewriteRoute package.
I am using a subfolder of web root to play with the ZF and was having troubles getting my controller to go to the correct place. After considering hacking both the Apache doc root and the actual Zend_Controller_Router code and writing a patch, I stumbled on the answer - Zend_Controller_RewriteRouter.
She includes the quick code that acts as a patch for the framework, letting it know that the directory it should be rewriting to isn't the root of the domain.