GConf is a system that was invented to make application preferences more manageable for system administrators.
GConf stores data in the user space in $HOME/.gconf:
- desktop/gnome for desktop settings
gconftool-2 is the GNOME 2 configuration tool. It is meant to be used from command line
$ gconftool-2 -R /desktop/gnome
That will display some of the GNOME desktop settings.
The GConf Editor is a graphical application and as such is more targeted towards the general user.