I am working on a hybrid live-cd/HD based remaster for server use.

Basically, all directories that contain config files and/or commonly writable dirs (/etc, /var/www, /var/lib/mysql) are symlinks pointing back to a single directory (in this case /bbix/var/www). Then, I can add an entry to the fstab file to mount a volume by label(LABEL=bbix /bbix auto rw,exec 0 0); if the volume is present, it will mount into the tree at /bbix, in effect overwriting the default configs and allowing changes to persist acrosss reboots. If no volume is present with the correct label, the mount fails and default configs are used. I am working on some python based install scripts to automate partitioning/labeling/rsyncing of the drive (also handling automatic set up of /etc/raidtab for mirroring)