Where does Compiz store its configuration in Ubuntu 12.10?

Solution 1:

All the settings related to Unity and Compiz are stored in the directory~/.config/dconf/ as a binary file user.

If you are looking to modifying the settings using the configuration file, you can't quite achieve that as it is stored as a binary file and is not human-readable. If tweaking the settings is your motive, I would suggest you use a configuration tool like Unsettings for that.