Here's another list! This covers
You'll need a place to back up to, and optionally a script/tool to help you/a reminder
I like compressing my files before backing up, but that's optional. There are utilities (I know Ubuntu has one by default) to do this for you, if you like! I highly recommend having a script/cronjob to do this for you, or using a built-in tool. If you don't have this automated, you might want to set up a reminder to do this regularly!
On a side note, also back up before you do anything major, like partitioning your drive.
The pain and anxiety you'll feel when you've lost something important isn't worth it at all. Please help yourself.
Concerning most non-hidden files in my home directory, my rule of thumb is that I should just know the contents of a file given its location and name.
I know it's tempting to name files temp, test, and foo, but that scheme isn't doing you any favors.
Go ahead and get in the habit of naming things in a Linux-compatible way. Don't include spaces in your file/directory names; it'll make any CLI thing with Linux painful. This bit comes back to the file organization concept, have a uniform way of dealing with natural spaces between words. Some folks like camelCase, others-like-hyphens, and others_prefer_underscores.
Unfortunately, there's not a one-ring-to-rule-them-all solution: camelCase doesn't work in React file naming, we can't use hyphens in Java identifiers, and you might have to escape certain files if they contain underscores in certain languages (LaTeX does this, if I remember right). Find a way that works for you, though, given that it'll probably change depending on what you're doing.
Begin your names with a non-lowercase character; no one has the energy to hit the Shift key every time (tabbing will take you through the rest!).
They're good for your computer (and you). Do 'em regularly (set up a cronjob or at least a reminder). :)
The docs are usually a great place to go for this! Also, you might be able to message the developer sometimes if you need a thing.
That, combined with forums and the official docs are your best friends in debugging. More often than not, the ArchWikis have a copy-pastable solution to whatever issue I'm having, no matter which distro I'm working with.
If you're making significant changes to an important file, make a copy of that file and name appropriately. For example, you could copy the file .bashrc to .old_bashrc, and then make all the changes/test to the actual file without too much fear. The file .old_bashrc won't be executed due its name.
Please, please, test your scripts on a set of representative files before running them on a whole filesystem with 100+ GB of files. This especially holds true with commands such as sed and recursive things. Ask me about "wtypeype" if you want to hear about my pain on November 30, 2018.
Git is probably the most common, and it's really easy to use. Please track your versions and commits with meaningful names; future-you will thank present-you when your code suddenly stops working.
You know how you're supposed to use visudo to edit the sudoers list, or run crontab -e instead of editing the file directly? Try to do the same thing as much as you can. Most of the time, these utilities tell you immediately if you've made a mistake in configuration, and they won't accept an incorrect configuration. This way, you won't be stuck with an impossible-to-debug situation, or worse, a brick. Don't even think about modifying low-level things like drivers.