Assume anything you can buy has a shelf life and set a yearly reminder on your calendar to copy forward stuff more than five or so years old, if those files are of significant value to you. Or for the documents, print them out—paper has better longevity than any consumer-available electronic storage.
That being said, quality optical discs are probably the best option in terms of price to longevity ratio for the average person right now. Just keep in mind that they are not guaranteed to last forever and do need to be recopied from time to time.
(I have yet to have a DVD fail on me, but I keep them in hard plastic jewel cases in climate-controlled conditions, and I've probably just been lucky.)
Actually, I don't think you could break a system in quite this way in Gentoo these days. Portage generally doesn't remove packages during upgrades (certainly not unrelated ones that would break the depgraph!). It would have exited with (in this case) a message about version conflicts before changing any packages and left it for the user to sort out. Modern versions of portage do a pretty good job of keeping you from shooting yourself in the foot by accident, while leaving you with a lot of leeway for doing so on purpose.