The Zend Framework being at Beta/RC means we are weeks/months away from complete fully functional applications that advocate a "final" best practice. Until then there's a bit of guesswork involved

, and everyone has their own way. One thing I do suggest is finding out about the Zend Framework conventions.
Conventions are essential in understanding how the framework developers intend the framework to be used and would have a significant bearing on a final directory structure. For example:
Conventional Modular Directory Structure
Not obeying the conventions has consequences. The more you depart from a convention, the more configuration and (hopefully unlikely!) subclassing may be needed to make the framework work the exact way you want it to. Another essential View convention was introduced with the ViewRenderer action helper which is enabled by default. It advocates defaults for template naming, view locations, and even the expected class-prefix for custom helpers and filters. Departing from these is troublesome to say the least. I stuck a quick solution guide on my blog a few days ago since it was creating havoc for some folk.
It would be best to ask more specific questions as you get started. These general pieces of advice don't always give you exactly what you're looking for

. I'd definitely start with the conventions, stick with them, and from these a lot of other things will fall into place more easily.
I have a tiny (read: deliberately miniscule tutorial app) application I recently updated for the ViewRenderer introduction. Because I did not know about this newly created View convention I had to re-configure it in my bootstrap file. Most of the directory structure is standard for a few of my more recent projects. Might be of some limited help.
Revision 14: /trunk