My current notebook system is a collection of composition books -- the cheap kind that one can get at a big box store for $0.99 a pop. Each one lasts me around a month. Once the book is finished, I go back and compile a list of topics and references. That'll work as an index, and since each book is only around 200 pages, it shouldn't take too long to find what I was looking for.
I only really use it for math at the moment, though.
The other system I have is a tickler file, except instead of the folders being days, they refer to whatever I need to learn more about before continuing on with whatever paper is inside the folder.
Each one lasts me around a month.
Is that why you are a paper machine?
I'm interested in keeping a notebook to check my ideas / knowledge on subjects. For example, if I wanted to find out whether there were anything in the notion of ESP that was worth merit, I could create a section titled "ESP", where I'd keep copies of research papers, critical commentary on methodology, questions, personal experiments if any, and so on. There might be some appendixes or cheat sheets with common errors in thinking and information about them, notes on the scientific method/philosophy of science, statistics formulae for estimating error and likelihood and doing hypothesis testing, maybe a few inspirational quotes. I'm pretty busy, so it might be a very backburnered project, but I feel like it could be useful. I can already see some benefits and disadvantages, eg it can be on subjects a person might like to keep private, like dating, overcoming psychological issues, sex, and so on, but peer review might not be as readily available.
Any thoughts on the format or arrangement for something like this? Is anybody doing anything similar?