Your personal data, once lost, is lost forever. For that reason, you should, at any time, have a good backup (preferably a few) anytime. That is the only data you need to worry about. All the other data on your OS is replaceable and repairable.
So you are good if you have backup copies of your Documents, Movies, etc. folders. Applications typically create hidden folders in your home folder to store configuration data. In some cases, there also may be data there you want to keep. For example, if you archive local mail in for example Thunderbird, you will also need to backup the data under
$HOME/.thunderbird/<your profile>.default-release/Mail/Local Folders.
In summary, just backing up your home folder, including the hidden configuration data of software, is already more than sufficient. You are fully covered as soon as you have a good backups of your personal user files.