I find foxmarks to be the best way to keep my bookmark data intact as
well. Now, I'd love a way to export or backup my thunderbird/pidgin
configurations as well.

However, a note of caution about keeping settings in your home directory
intact between upgrades using the 'clean install/restore' method.
Sometimes it is the settings in your home directory that cause the
problems. I always run a full gambit of tests on the system to make
sure it is working before I restore, that way, if it breaks after my
restore of /home I know it was something in there.