I don't know what I'd do without Text Block Writer, a fantastic piece of free software that I downloaded at Software by Brian. A writing club member recommended it in a message board thread about "advanced writing techniques" six months ago (thank you, whoever you are!) and I've been using it ever since.
This picture doesn't begin to do it justice. It is a "virtual index card" system that allows you to arrange and rearrange paragraphs, sections, or chapter headings, in order to get a handle on the overall organization or logic of your argument, chapter, article or book. I don't even use it to the extent that Brian suggests on the site (he's even written a book about how to use it to write a book, which I haven't read.) His recommendation is that you can write the whole thing in the little blocks, then export it all to Word or another program.
You can decide how many columns you want, you can minimize the little blocks until they are just titles, or small blocks, or enlarge them to bigger squares, and then you can move the blocks around. There is also a super-block for headings, and a space for notes and storing unused blocks.
I'm writing a book, tentatively called Do You Deserve a Ph.D.?, which is aimed at graduate students, and explores the psychological blocks that stop them from succeeding. I find that the organization of the book is one of the most difficult areas for me, and Text Block Writer has really helped me get a handle on that. A big thanks to Brian!
So dissertation writers, book writers or any other writers, if you are stuck, confused, or overwhelmed by what you've written so far, download this baby and start labeling your paragraphs and sections. It's amazing what moving some text around can do for the logic of your argument.