Pharo 3.0 is prepared for final release these days. One of the latest updates included a small tool called "Versioner". It had to be loaded separatly but now found its way into the standard image.
This tool allows you to help versioning your packages with Metacello configurations and should help you dealing with versioning all your ConfigurationOfXXX classes.
Christophe has written a short docu on the tool. Nice!