I don't know how it works for other distributions, but Debian mostly ignore whatever the default paths for an app are in favour of consistency across all apps in the distribution.

And how does this map on to Windows? Or MacOS X?

It's not up to us decide that sort of thing globally - it's down to whatever makes sense for the particular platform the package is targeted at.

I would suggest for Linux and other UNIX-like platforms, that we adhere to the Filesystem Heirarchy Standard (http://www.pathname.com/fhs/pub/fhs-2.3.html). Most vendor-related files should live under /opt.

Based on the FHS, I would expect to see the layout like this:

/opt/ZendFramework/doc => this is where the ZF manual and api doc lives
/opt/ZendFramework/lib => this is where the ZF class library lives
/opt/Zend/ZendFramework/lib/tests => self-explanatory
/etc/opt/ => stores ZF-specific config files
/var/opt/ZendFramework/ => stores ZF-specific temp files, cache files, log files, etc.

The incubator is tricky. I wouldn't think it should live together with production-ready ZF files. So providing another package for it makes sense, e.g.,

/opt/ZendFramework-incubator/... (same hierarchy)

Mac OS X seems to have its own conventions, e.g.,

/Library/Zend Framework/doc
/Library/Zend Framework/lib
/Library/Zend Framework/lib/tests
/Library/Zend Framework/etc
/Library/Zend Framework/logs
/Library/Zend Framework/temp

/Library/Zend Framework incubator/... (same hierarchy)

On Windows, what I'd choose is:

C:\Program Files\Zend Technologies\Zend Framework\lib
C:\Program Files\Zend Technologies\Zend Framework\lib
C:\Program Files\Zend Technologies\Zend Framework\lib\tests
C:\Program Files\Zend Technologies\Zend Framework\conf
C:\Program Files\Zend Technologies\Zend Framework\logs => for logs
C:\Program Files\Zend Technologies\Zend Framework\temp => for ephemeral cache files

Likewise, incubator gets its own matching heirarchy:

C:\Program Files\Zend Technologies\Zend Framework incubator\... (same hierarchy)