There is unlikely to be one best way to organize your thoughts. How you ought to proceed will depend on a host of factors. It could depend on: you, your background, the subject, its depth of treatment, and the audience. The concern, here, is with a more modest question of the best (open source) software to use in helping organize your thoughts.
This text is being composed with the help of RoughDraft. I know what I want to say, more or less, ... it’s a question of getting the (electronic) words on (electronic) paper. RoughDraft was designed as a simple tool that would not get in the way of moving words from head to paper. It’s no longer being updated, but the available version has all the basic tools that a writer needs. It supports standard rtf text formatting, with handy writing tools like multiple notepads and clipboards, and includes a calculator. It’s not a full-blown document composition system, but it does provide all of the writing basics in a small, efficient package.
When you don’t know quite what needs to be said, the challenge is to discover or develop the basic pattern (form / structure / architecture) of the presentation. What should be included? What supporting information is required? What’s the best order of presentation? Once the basic pattern has been clarified, any comfortable writing tool can be used to go from pattern to words on paper. What’s “comfortable” is obviously a personal choice. For this text, I chose RoughDraft.
The first tools to consider for more complex arguments are outline processors. Full-blown word processors like Microsoft Word or OpenOffice Writer do include outline processors, but they demand more refinement that I find appropriate. I prefer a simpler outlining tool. I’ve searched for a good, free outline processor. There are several, e.g. KeyNote, KeepNote, or SEO Note, but none of them have quite the features that I want. My Notes Keeper is the least expensive (at $29.95) outline processor that has the features that I want. It provides a quick and easy way to build lists and sub-lists and sub-sub-lists and so on. But it’s a strongly one-dimensional view of the information you gather - items naturally move up or down in the list.
When I’m searching for the right pattern, I really want a more two-dimensional view of the material. FreeMind is a popular open source graphical concept mapping tool. Think of it as a two-dimensioinal, graphical outline processor. There is even an “academic” version called SciPlore MindMapping that has the extensions required to support full academic referencing. It fits the bill when you want a more flexible, free-form kind of outline processing.
Some people have found that wiki system is useful in helping them get it all on paper. The problem I have is that no patterns may jump out at you once all the links have been established. I need to work at my patterns, often being required to go in search of new pieces of information in order complete a pattern. Wikis don’t highlight the pattern in a sufficiently forceful way. I see their value when the opinions, insights, and concerns of multiple individuals need to be considered. But for one person, struggling to find the pattern, wiki doesn’t provide enough help.
If you want a full two-dimensional picture of the information, I’ve found two possible open source systems, VUE and Compendium. VUE stands for Visual Understanding Environment. The system was developed at Tufts and they are maintaining it. Nodes can have whatever shape and colour you fancy, with attached Text and Keywords. Notes can connect to other notes with links that can have labels, text, and keywords. And everything is laid out in a two-dimensional picture. Compendium is a somewhat different beast. It comes from the Open University in the UK and assumes that every map can be organized in the form of Questions, Answers, and Pro and Con supporting arguments. Most topics of interest could be formulated as Questions, but it’s not very natural in many cases. VUE is closer to what I find comfortable.
A final tool that I find useful is a diagraming system. Microsoft has Visio; Dia is a similar system, but it’s open source. If you want to draw a “pretty” picture of the pattern you have discovered or developed, Dia is a good candidate for the tool of choice.
That’s it for me. RoughDraft for blasting words on paper. My Notes Keeper for organizing notes, i.e. outline processing. Then VUE to develop two-dimensional picutes of emerging patterns. And, finally, Dia to build a pretty picture of the pattern you discovered.
End Note: Doing a Google search on the names of any of these systems will lead you to their home webpages. Including URLs seemed like an unnecessary extra.