Since I am working on PloneSoftwareCenter to make it PyPI-compatible, I have worked on distutils side to make the register and upload command more friendly when an egg has to be registered to several servers.

The problem with the actual .pypirc file is that it won't let you define many username/password for many servers: it is dedicated for one server. In the meantime, you can specify in a command line option which server you want to deal with:
$ python setup.py register -r http://my.server/pypi

But this will take the username/password in .pypirc. So if your username differs from one server to another, it won't work.

I have worked on an enhanced version for this, described here: http://wiki.python.org/moin/EnhancedPyPI

The patch is ready, and comes with new unit tests register and upload commands didn't have yet. The new .pypirc format was shaped with the help and feedback of catalog-sig people, thanks to Martin v. Loewis and Fred Drake and others. I am going to submit it for inclusion today. If it is accepted and integrated we will be able to deal with our eggs like this:
$ python setup.py register sdist upload # goes to PyPI

$ python setup.py register sdist upload -r plone.org # goes to plone.org ;)

The next step is to provide a patch for a permissive trove classifier in PyPI. Then all PyPI-like servers will be able to provide the same service for egg developers, no matter how they deal with classifiers.