Its the matter of standard but...
searching for application preferences is a bit strange. I think it would be nice to see something like that

/home
--/common
--/defaul
--/root
--/my_u_name
----/preferences____here should be all application files saved
----/music \
----/documents | All of this kind dirs should be symlinks
----/video / with internacionalized names. User should be asked at firs logon where he wants to keep this things (e.g. some people prefer to keep documents on /media/ntfshitty to be able to read documents when they use xp)
++Computer
----/System
------/Applications
------/Libs
------/Documentation
^^System should be also virtual directory with gobo like symlinks generated at every dir refresh. Its not for administrative purposes like in gobo - I think rather about something what will simplify acces to these things for users withought sudo priv`s
It`s easier to sort list of those things in nautilus visrtual directory than thousands of duplicated (versions&symlinks) little files in /usr/bin