There is an interesting program available for OS X on the Mac. It's called "Scrivener," which is described as a "word processor for writers." Many people have asked for a Windows version of this application, but, as the developer has made clear, a Windows version of this excellent program will not be forthcoming because OS X is internally so different from Windows that it would require programming it from scratch.
Naturally, people have searched for windows programs that come close. The ones mentioned most often are:
Liquid Story Binder
I tried all three, but none of them really appeals to me. There is, however, an application that I have used for a long time and that I have recently realized can be used very much like Scrivener. This is ConnectedText. Let me explain.
Scrivener is a program that is intended to integrate the process of research, outlining, storyboarding and writing. ConnectedText is much better as a repository for research, has an outliner that is almost as capable as Scrivener's, and it allows you to write distraction free, in the same way as Scrivener. While it does not have a "storyboard," it does have a Navigator that can fulfill a similar function. It also allows you to write in full screen mode. In addition, it has something that Scrivener lacks, namely the ability quickly to link entries by using wiki links.
All you have to do is to save a desktop of the sort that I have illustrated in the following screen shots. This desktop for writing has two panes: one for writing, and one for navigating, containing views for the Outline, the Navigator and the Table of Contents (for the topic on which you are working). This is the screen with the outliner and a topic in edit mode:
This is the screen with the navigator and the topic in view mode:
Scrivener is thought to be the word processor for the "non-linear" writer, i.e. those who do not compose longer pieces by starting at the "beginning" and ending at the "end," but those who compose different parts of the piece and then later worry about where they fit. These are also writers who do not make a clear break between a "research" and a "writing phase" in their work, but do both in tandem. ConnectedText approaches researching and writing in the same way. This should be equally appealing to those who have to write academic texts as to those that write non-fiction.
Neither application is meant to prepare the final copy of the text. Where Scrivener uses "restructured text," ConnectedText uses a wiki markup that is close to that of MediaWiki's and can easily be transformed into html. There is a rudimentary macro on the Website that allows transforming the markup into rtf as well.
One area where ConnectedText really shines is version control. Every revision of every topic or note you write is kept. You can, accordingly, measure the "progress" you have made in developing your ideas, paragraphs, or papers at any time.
I know no better alternative to Scrivener on windows than ConnectedText.