I’ve been looking for a lightweight outliner program to handle my piece-meal thesis work. I discovered Maple, which seems to be what I was looking for, from this list of outliner programs for Windows.
It lets me organize my writing into manageable sections, then easily work on each once I have the sources at hand. Also, I can export the tree as a flat file in doc, txt, html, or rtf.
In my ideal world, it would have support for footnotes or endnotes, but I guess you can’t have everything.