gconf

..in fact, gconf really is excellent. It:
- Has an underlying XML filestructure, which is possible to manually edit (though not so good as the .ini format), and these files can be copied around like other dotfiles.
- Has a CLI interface, gconftool-2, which lets you get and set certain keys. This is REALLY(*) useful.
- Can support changing settings in real-time (across multiple instances of the app without restarting the app, and even without needing an "Apply" button).
- Has a GUI editor: gconf-editor, which is useful for finding the keys whose name you don't know.

(*)For example, I've set up a new system. I want to preserve most of the system defaults, and especially if there is a new feature I don't know about, I don't want to remove it from the conf-file. But there are about 20 settings I really want to keep. So I have a script with lots of lines such as:
gconftool -t string -s /apps/metacity/general/button_layout 'menu:minimize,maximize,close'
I can run these commands inside a running GNOME session, and they immediately take effect.

[Sadly, KDE doesn't have such a system, as far as I can tell. It's impossible to script the setup of a KDE system in a non-brittle way]