If I understand the question you want to copy settings from old system to the new one. In my backup scripts I just copy ~/.gconf directory which store all the settings configurable with gconf-editor. That works for me.
There are other directories for settings of your GNOME desktop environment which you may want to copy:
~/.config - contains config files for applications (default location for the environment variable XDG_CONFIG_HOME).
~/.gnome2 - user-specific application data that is not stored in the GConf repository.
~/.local/share - default location for the environment variable XDG_DATA_HOME.
~/.fonts - fonts that you installed.
~/.nautilus - contains file manager data that is specific to the user. For example, this directory can contain the following:
- Metadata for the directories with which the user works.
- Nautilus emblems that the user adds.
- Nautilus desktop images.
~/.themes - contains your (not system-wide) themes