Free software doesn’t need to be backed up. If you lose a hard drive you buy another one and re-install.
On linux systems what I do back up are the /home directory and /var/www/html (where I do web development). I like to copy my /etc/fstab and /var/spool/cron directories too but they never change, so one copy is enough.
I have two internal hard drives (three actually). OS on an SSD, /home on a six terabyte WD red drive and another 8 terabyte WD that mirrors the first.
Heres’ my crontab
# m h dom mon dow command
0 0 * * * /usr/bin/updatedb
0 1 * * * /usr/bin/rsync -avz --exclude 'cache' /var/www/html/ /disk1/www/html
0 2 * * * /usr/bin/rsync -avz --exclude 'cache' /home/ /disk1
…where disk1 is my backup mirror disk
That rsync takes a long time to run the first time but quickly thereafter.