Letting the user place the config files may be disadvantageous (and Urxae is right... where to store that info, in the registry?
)
%APPDATA% is really the place that is designated for that purpose under Windows, it works like a charm, too.
When I lately got a new PC, I just copied the Thunderbird and Firefox folders from %APPDATA% over the network, and I had all my email and all my settings on the new PC. That is really how software should work
I wish Office worked that way, too!
Under Linux, I think that ~/.bash_profile, ~/.fetchmailrc, ~/.gnome, ~/.ssh, or ~/.mozilla are good examples for a scheme that works and that each user is able to understand.