I have a folder in my home directory called "configs". Once I get my box how I want it, I back up my XF86Config, lilo.conf, kernel stuff, rc.local, and other things to that configs folder. That way if I have to reload ever I can reload, update the kernel, and copy my junk all back and reboot.
My /home directory is mounted on a different partition. That way I just don't format it when i reload and it's all still there