I would say that you should be fine with some/most/all of /etc and /home. I usually backup these, as well as /usr/portage/distfiles and /usr/portage/packages - those help save a bit of time on downloading and/or compiling
As far as the /home and /etc backups, I usually go through a minor period of adjustment, making sure there weren't any packages that got updated behind my back while I wasn't looking, and maybe have config differences. Long story short, I usually follow the above and then interactively restore my previous configs over a few days.