Well ultimately I would like to see nothing in the /usr tree at all and certainly no configs in /etc. All apps should go into /opt as per optification rules to avoid using rootfs space. No configs should go into /etc that are not daemons or system level software. I much prefer the config in the user space.
[sbox-FREMANTLE_ARMEL: ~/pyPandora] > which pianobar /usr/local/bin/pianobar [sbox-FREMANTLE_ARMEL: ~/pyPandora] > ls -al /usr/local/bin/pianobar lrwxrwxrwx 1 maemo maemo 33 Feb 9 08:07 /usr/local/bin/pianobar -> /opt/maemo/ usr/local/bin/pianobar