As with anything on a computer, the best thing to do is backup all the main files, except for the large images, videos, music, games and manual folders.
Just copy them to another drive on a regular basis and if there are any issues you can simply copy them back from your backed up folder and replace existing folders.
I do this on a daily basis and it's approx 10gb for me and I have 150,000+ games (takes 10 minutes to copy files)
Very useful if I start messing with settings etc and any issue arises.