Currently, there is no simple way for backing up specific gconf settings (as opposed to backing up the entire registry).
For example, suppose you want to do a clean install of Karmic and would like to preserve your gnome-terminal, nautilus, and empathy settings, but nothing else. To backup a single one of the above settings by itself might involve a large number of steps. To backup and then restore your gnome-terminal profiles, for example, you would need to:
1. Backup the specific gconf files from ~/.gconf/apps/gnome-terminal/.
2. run gconf-editor on the new system.
3. Navigate to /apps/gnome-terminal/global/profile_list
4. Edit the value of profile_list, click on "Add" and then enter the names of each of your profiles.
So in short, if a user doesn't wish to copy of their entire gconf settings, it quickly becomes a large production.