GConf files aren't binary; they're XML. It may not be the greatest format, but it's editable and rgrep-able, and gconf-editor documents many of the keys. Sometimes it's good to declare One True way of doing things just so you know what to expect, and if GConf really doesn't work for your app, you don't have to use it; there are still plenty of GNOME config files outside .gconf/.
I have played with Gnome config files a couple times and never quite appreciated their organization. With all due respect (I never contributed a single line of code to Gnome) I think that keeping config in lots of human-friendly formats such as yaml is a better solution than grouping stuff in XML files.
It's not nearly as bad a solution than the Windows Registry, but it's not perfect either and has some good chances it's not a step in the right direction.
