Comment by mindcrash

My strategy for Gentoo, more or less:

/etc/ - all modified configuration files, including

/etc/portage/ - make.conf, package configuration (package.accept_keywords, package.use, and friends)

/var/lib/portage/ - world, and world sets. basically everything portage needs to rebuild the system

/var/db/repos/ - notably local and/or self-owned package repos

/home/<username>/ - no explanation needed

/root/ - no explanation needed

This should contain enough to pretty much rebuild a Gentoo system from a clean downloadable Stage onwards without (too much) intervention.