> However, on the desktop, many different application want to read and write keys. Tray applets, the system config panel, even your media player...
If your applications directly read and store configuration keys belonging to other applications, you have way worse problems in your architecture than configuration file format.
Configuration items like current theme or current default font are things, that all applications are interested in. If they want to have look and feel like the rest of the desktop, that is.
That opens another can of worms: What is system control panel: is that gnome control center? Or command line dconf tools? Or is that dconf-editor? Or one of the myriad tweak utilities?
Cut off one of these and brace for the whining, that gnome is dumbing everything down and locking up your settings.
If your applications directly read and store configuration keys belonging to other applications, you have way worse problems in your architecture than configuration file format.