Clever PHP Application Organization Structures?

Question

There are a million-and-one file-system structures that go into the myriad of Open Source projects available. Things like modules, language files, domains, third-party libraries, migrations, internationalization, backups, and syslinks to other parts of the system have given rise to many approaches to organize the filesystem of a project.

As a PHP developer I'm wondering if any type of standardization is starting to emerge among projects. With PSR-0 we finally have a standard for naming and loading files - but it nothing to my knowledge about the rest of the components that make up the system or how they can be handled in a sane way.

We are dealing with a lot more than just MVC, so what examples are there of large projects correctly handling all of these things?