For collecting notes, some people just use their word processor. But word processors are meant for authoring individual documents, and are not very well suited for working with large collections of short notes that are often related to each other in numerous ways.
Personally I divide my notes into two general types:
- unstructured: random notes about things that might be useful, but which are not yet part of any coherent project
- structured: notes that are all part of one general project — a research project, a course, etc
Working with unstructured notes
For notes of the first type, the two crucial requirements are that it will be easy to enter new notes and easy to find them later when you need them. The first requirement is easy to meet; the second one is more problematic — we've all found ourselves sitting in front of our computer and mumbling "Where is it? I think I put it here... no... maybe here?... no... I know!!... no..." etc. What you want is a tool that gives you as many ways of locating your notes as possible: searching for text, following hyperlinks, using tags/keywords, etc.
Personally, I use my own private Wiki. Even though wiki software is meant mostly for collaborative projects, where many people are collectively involved, a personal wiki is a very nice way of keeping your own notes. With a wiki, you can easily create links from one note to another, and searching through your collection of notes is very simple and efficient.
To build your own wiki, you need a piece of software known as a 'wiki engine'. There are dozens of free wiki engines that are totally free, but some of them can be quite difficult to install. My personal favorite is DokuWiki, which is extremely powerful and flexible. If you want to give it a try but find the installation to be too complicated, you can try this option.
Some other relatively easy to use options for a personal wiki:
- MoinMoin
- another wiki engine that is relatively easy to install
- Zim
- a very easy to use 'desktop wiki' for Linux
- VoodooPad
- a desktop wiki for Mac OS X
- Wikidot
- a friendly online hosted wiki; also great for shared academic projects
- More
- see this list
Working with structured notes
For structured notes, I prefer to use some sort of hierarchical notebook, in which I can always see and rearrange the hierarchical organization of my notes.
My favorite tool is the brilliant emacs package org-mode. Yes, it's aesthetically ugly, and learning how to use it requires a non-trivial effort, but it's really worth it. I recommend this very nice video of the original author of org-mode, Carsten Dominik, explaining what it is and what it's good for; as he explains, he created it as a tool for his own academic work, and once you start using it you immediately see how different it is from all the mainstream tools, whose developers don't really understand or care about the way people work in the academic world.
Two other tools I've used in the past are:
- NoteCase
- Good for notes that are just text
- TreeLine
- Good for notes that have some fixed internal structure; it's like a hybrid between a hierarchical notebook and a database
Finally, another excellent option for Mac users is Scrivener; I used it briefly before I switched from using a Mac to using mostly Linux.
