A few months ago, Robert Basic wrote about this handy organisational tip:
Thanks to a discussion on the Zend Framework mailing list I learned about a new feature, a feature that allows for grouping action controllers in subdirectories!
He then goes on to explain how he can now group controllers related to admin within a subdirectory of controllers which makes organisation easier:
Best part is that this feature requires no additional configuration. Create a subdirectory under the controllers directory and place the controller file under that subdirectory. In that pretty screenshot image you can see a FooController.php in the directory called Sub; the class name in that example is Sub_FooController and is accessible via the sub_foo/controller URI. The corresponding view files should be placed in views/scripts/sub/foo/ directory.