It seems that the site is populated by people who are thinkers, and who use the computer to think well or better. I wonder if we might not learn something if we shared the process we go through individually to write a paper. Here's my contribution:
I use Inspiration--
I rough out the ideas by using the graphic mode to enter as many things I can think of that are relevent. Then I drag related ideas into separate areas of the screen. Then I think about a label or category for these ideas and create a graphic for the unifying idea. I then use the link tool to link things up. Finally, I click the outline button which brings me to an outline of what I've roughed out one level deep. From here, I put the meat on or take it off the skeleton so to speak.