Oooh, this looks like a good read! It's fun to read how other devs organize, so I can steal their good ideas.
Right now I'm a mix of Trello boards, Google Docs, and physical notebooks with to-do lists and design sketches. I can get away with a lot more of that because I work solo 95% of the time, though.
...That said, no amount of organization will get the actual work done.