dpkg-repack the entire system plus recursively copying $HOME (with or without MyDocs, configurable) should do. dpkg-repack would get the current configuration files and when installed again you'd get you system back and running exactly as before.

dpkg-repack is on extras-devel. It should not be difficult to build a backup utility as the one you said.

Excellent idea, by the way. Although I think you're exaggerating when you say it's not "The Unix Way".

OBS.: I know of no such utility as dpkg-repack for RPM. Does anyone know?