Howdy. For the combination, Tinderbox seems to offer the most. But in reality, I am finding that DevonThinkPro is the best repository for all documents, and Tinderbox is the thinking, linking, and analyzing application (and aliases offer additional possibilities, and you can even code the attributes and use prototypes). I have both applications, but have been working in Tinderbox for the past month getting more familiar with it. Tinderbox allows many different views (Outline, Map, Tree, Chart, Timeline, HTML, Nakakoji, Explorer). And it can be exported as RTF or HTML. You can import PDFs and images as well. There is real power and flexibility with it. I have only scratched the surface, but I will never outgrow its power. It will help if you read the documentation online, but especially the book, The Tinderbox Way by Mark Bernstein who is the coder, program developer, marketing, etc.
It seems that many are using both DTP and Tinderbox in combination. That will be my eventual goal.
For writing a dissertation for me, my final step would be Mellel (because I use Hebrew, Greek, Latin, and German, along with English and Mellel handles them very well). And it never chokes, no matter how long the document. And Mellel has multiple note streams.
