I implemented a simple command line feature that allows you to specify alternate configuration files. Usage:
pypanel [-c file]
I also decided (mainly for my own purposes) to only allow one configuration file to execute, rather than including both the user's ~/.pypanelrc and global /etc/pypanelrc files as it was before.
There is a fall-through mechanism so that if any configuration file does not exist, the next best option will be used (argv > user > global).