Most everything is going to be stored in your home folder. Though conflicts may
arrise just saving that does a world of good. The next is the /etc directory.
That I would not directly copy but keep so referene so you can configure what is
needed by hand when the GUI fails to do what you want.

After that anything in /usr/local where custom compilations go. Then save and
custom package files to install, I would also back up your grub settings from
/boot/grub/menu.lst just in case.

After backup then wipe and install the new OS and restore just data - no
settings. Then restore settings as needed.