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.
It seems like Evernote is what you want. It allows you to take notes and link pages, and it's free up to a fairly high amount of data storage.
I would like to chime in that this is a really good piece of software. I've thought about writing an entire discussion post about how much this helped me "get organized" after trying many other solutions.
If you have a smartphone, you can sync photos of any important papers, notes, signs, menu items, etc. to the Evernote servers, where they will not only be immediately available from your other devices, but they will also be automatically text-parsed and the text made searchable. So even if you were lazy and, say, snapped a picture of your rental contract before you signed it, but didn't label this photo, you will be able to find it again just be searching for keywords like "contract" or your apartment name.
It also records voice notes and then text-parses the notes if they are relatively short. Of course this text is also searchable.
I have the paid service which allows you a larger amount of data storage and allows you to upload and search pdfs, which is useful if you want to use it for academic research.
Additionally it's very well supported, Evernote just going to keep getting better and better over time. I was kind of annoyed that their pdf text searching function didn't work very well, and then later realized that they had upgraded it.
I spent literally months trying to learn to use org-mode, then I tried to implement GTD inside Evernote, and had a working task management system within a day.
I read in a biography that Isaac Newton kept a notebook system under headings for different topics like an encyclopedia. As for myself, I can never manage to write in a notebook or diary for more than a week, but I always feel that the idea would be a good one.
For the record (or whatever) I used to keep a set of composition notebooks like paper-machine describes. They got to be a really huge number, some of them redundant, most of them mostly empty or only a third full. A few of them got to the point of being all the way full and spread into a second volume. They mostly contained lecture notes from my college classes, sometimes I'd get up the energy to add additional notes from studying into them. I threw them out sadly, a few moves ago, when I was depressed and cutting down on my possessions to try to get more control over fewer of them. That was my rationale at the time, anyways. There wasn't much of a system of organization to them though, except that it would be one subject per notebook, summaries of whatever I was studying on one thick column and notes about it or things that popped into my head while I was listening or reading in the other column.
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?