Ubuntu – Where are theme and Compiz settings stored

gconf is deprecated, so for a new project I would not use it. dconf is a backend for storing the settings, as an application developer you should normally not have to bother with it.

What you seem to need is gsettings, a high-level API (API documentation for C) to store/retrieve settings without bothering how/where they are actually stored. gsettings is part of gio, which is one of the core packages of gnome (like glib and gobject). This blog post gives a short introduction how to use it with Python.

If you do not want any dependencies on gio (e.g. you are not developing a GNOME application) and want to store simple config files, I'd suggest to use the $HOME/.config directory (or whatever directory defined by $XDG_CONFIG_DIRS) instead of $HOME/.your_appname, in line with the freedesktop spec.

It depends on your set-up. They are stored in several locations. The best way for you to find them is to open your Terminal Ctrl-Alt-T, then type sudo locate compiz and press Enter. It will return several results, but you can tell by the names which will contain your settings.