A number of people on the mailing list and twitter recently have asked how to autoload Doctrine using Zend Framework's autoloader, as well as how to autoload Doctrine models you've created. Having done a few projects using Doctrine recently, I can actually give an answer.
His short answer - "attach it to the Zend_Loader_Autoloader". For those needing the long answer, he goes through a simple example of creating the loader object, registering a new namespace and pushing in the Doctrine functionality as an autoloader. The bootstrap class can then be modified with an "_initDoctrine" method to pull in just what scripts your app might need.