I have 3 - 4 pocket notebooks at any time. Added together, I now have a box full of tiny notebooks, it's great. So much material to look through and draw inspiration from. On the day to day, I'll keep one main notebook in my pocket, and a few more organized by subject kept around. A friend recommended the Bullet Journal Method. It's worth reading through and taking notes.
Notebooks and journals are great, its an important meditative practice. I filter information from my pocket notebooks into my larger journals and continue the ideas on a bigger page. As far as binders, I think about them like databases, and indeed want to write software that mediates a digital - physical copy union between a binders and databases. I tab out binders completely, and create an index in the front. That doesnt keep be from litering everything with doodles.
I found Cherrytree when learning about Kali, how people use it to organize data either from a black hat standpoint or for gathering information about perps from a white hat perspective. I tried it and have used it ever since, it's a perfect example of what open source has to offer. You can use cherrytree for any of a thousand things, after all its just a databasing program that stores nested information. Cherrytree is a permanent dailydriver for me, you can't beat its simplicity.
I'm slowly flushing out a personalized linux experience, and dropping the scripts on github! Bash toolchains are just a chill way to code, I've found and instantly patchable into any system I'm using. I've recently looked into JQ and have realize its going to be a tool I'll be scripting with constantly. As far as code I'd like to be writing, I want to be leveraging json manipulation to create handcrafted tools that quickly, easily, and better yet, universally import and export code.