One trick is to look at the gconf settings for apps, such as the screensaver, nautilus, panels, etc. Often there are tweakables in there that aren't exposed in the app's preferences settings.
Run gconf-editor for a GUI interface to examine config settings, or if you prefer command-line tools use gconftool-2.
For instance, I make a script to customize a new Ubuntu install (I'm frequently installing/reinstalling and like to have the look and feel customized to my preferences automatically). I use gconftool-2 to do all these customizations. For example:
gconftool-2 --set /desktop/gnome/session/idle_delay \
--type int 30
gconftool-2 --set /apps/gnome-screensaver/lock_enabled \
--type Boolean FALSE