Well just now using Zend Framework i would structure my app based on my 
documentation and my experience in the following way.

application
  layouts
  configs
  models
  controllers
  modules
    default
      models
      views
      controllers
    forum
      models
      views
      controllers
    stories
      models
      views
      controllers
    blog
      models
      views
      controllers
    gallery
      models
      views
      controllers

This allows the sub applications to work with the main application, now 
i am not quite sure how i would do something similar to logically 
separate the sub applications with Rails.
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