It depends. At work among developers, we use a local directory with different paths for different systems and architectures

/repo/Ubuntu/8.04/x86_64
/repo/Ubuntu/8.04/i686
/repo/Ubuntu/10.04/x86_64
/repo/Ubuntu/10.04/i686
[download]

etc. Each computer knows where to search for its libraries, and there is a special cpan wrapper that can install a package for all the combinations.

For shipping one application, we use darkpan on Linux, but cpan on Windows (Strawberry, previously PPM with ActiveState).

And so on.