I believe it's important that we don't let this become like other open-source operating systems - cluttered with various setting files. We need to create one settings manager that all programs will store their settings in. With Ubuntu, if you want to change the font everywhere you have to change it in appearance preferences, gnome-terminal, ~/.profile, and others. We need to avoid madness like this.
Another problem with common setting managers is that they don't integrate very well with the OS - there's no way to make a shortcut to the current desktop background for example. We should store our settings in files, one setting per file, that way it would be possible to take advantage of links and any other future filesystem features.