I am compulsively organized, to a fault. When I play video games, I make spreadsheets and notes and track everything by hand. Right now I'm playing through Final Fantasy X for the nth time, and I have a spreadsheet showing instances remaining on each character's overdrive mode learning. For each type. So every time Lulu evades, I reduce the number by one in her "Dancer" row. Every time Wakka lands a status effect, same thing for his "Tactician" row. Sometimes when people watch me play games, it drives them crazy. Makes for very thorough speedrun routing, though!
I'm sure some here by now are familiar with (and annoyed by) my use of Notepad to code my big game project, but it's what I have to use, since I often do coding during downtime at work, and I can't use outside software. So I'm up around 6000 lines of code now, in Notepad. You don't manage that kind of thing without strict organization. All my routines are indexed and categorized, whitespace is used for visual clarity everywhere (the QB64 IDE would actually ruin this), and my folders are all where they are very much on purpose.
Being so organized takes time up front, but I reap pretty huge benefits later on. When I have to debug, it takes me maybe an hour or two at most, since I've already built in quite a bit of tools to let me see how data is being handled - such as a good old fashioned "debug menu" where I can scroll through the spawned entities and watch their data, edit player health, ammo, available weapons, turn on hitbox display, all during runtime. I even have a rudimentary level editor, minus some abstraction - it's really only meant for me to use.