If you can, back up EVERYTHING.
Otherwise, have a single folder to back up, and just save everything you'll need to keep in that folder. For me, that's usually just my home folder, as it's where all of my configs / data are saved. Everything outside of that is just a bunch of apps which I can easily reinstall.
Also, this is coming from someone that lost everything 2-3 times, so if it happened again, I'd get over it within a week.