I am using a writing program called Scrivener for my academic work lately. It is a very compelling program for academic writers, because it allows for the construction of documents in a very non-linear, non-top-down approach. As I research for an article or chapter or paper for class, I can add parts of the document and not worry about how those parts are connected to the rest of the parts. After I have all the parts laid out, I then start to see connections and can begin to assemble the piece in a way that provides a sensible narrative.
A fellow academic has produced a tutorial outlining some of the features of Scrivener and why it makes sense for academic writibng over a more linear approach such as a word processor. Word processors are great for 2 things I think: relatively short documents such as letters or short papers where there aren’t lots of pieces that have to be interconnected. They are also great for the final assembly and polishing of a manuscript. I like Scrivener for the ability it has to produce the manuscript from bits and pieces of thoughts.
Here’s the tutorial: Five Essentials Tutorial