Where can I find a Unity configuration file?

Unity and Compiz are using GConf to store their settings. GConf is a configuration store that provides an API for applications to read and write configuration information and receive notifications when configuration items change. The configuration data is saved under ~/.gconf, but modifications should only be made through the GConf daemon.

You can modify the Unity settings directly using gconf-editor and browsing to /apps/compiz-1/plugins/unityshell/screen0/options. You will notice that Unity responds to changes instantly, the same as CCSM.

If you want a command line tool to modify these settings, use gconftool-2. For example, to reduce the launcher icon size I can do:

gconftool-2 --set /apps/compiz-1/plugins/unityshell/screen0/options/icon_size --type int 32