It would depend on the type of app but for me, it's mainly web apps. If one of my web apps get's huge, I take a hard look at the namespace (http://www.foo.com/webapp) and see if I can break it out into parts. For example, for a typical CRUD database app, I may do:

and then instead of all the logic (model,view,controller) being in one big-old-module (webapp), I would transition as much as I could to new modules which hold the logic for each piece of the app (with appropriate commonality in a webapp superclass). So the object hierarchy may look something like this in the file system: