To keep all the applications, OS modifications, hardening, config, etc. When I used Windows, I used one partition for OS/apps and one for data. I backed up the data in a straight-forward, file-level way. Did the other partition as a whole with Acronis. Periodically restored from clean state, did updates, backed that up. So whole system was always one restore away with critical data available with secondary box until that finished.
"If I had to, though, the first tool I would reach for would be `dd`...which the author never does, because it's too archaic, unlike those fancy GUI programs that don't work?"
dd, Gparted... not sure what old stuff like Acronis or Ghost do on modern hardware. I use non-SSD disks on older laptops and servers so I'm not sure. On Linux past few years, I just backup key files and clean-slate install when I have problems because a reinstall/re-config is quicker than a differential backup on a Windows box. :)