I wrote my PhD proposal, some 40 pages with nearly 70 references in OpenOffice. Outline numbering and Bibus based referencing worked out quite well for me. There were some tricky times with equations and such but I managed to keep it all together in the end.
Now I am facing a much larger task of writing a few hundred pages. So I started at the obvious point, adding pages to my proposal. Ideally the proposal should form the first chapter regarding background, before I delve into my core research. After 15 pages or so my outline numbering began to fall apart and I decied to look elsewhere for a more reliable solution.
So far Miktex with WinEdt has been doing the job remarkably well. The bibiliography comes in from Bibus as a management tool in bibtex format. Terms can be managed using the glossary tools - which I haven't managed to persuade into action so far. Google docs can be repurposed to be an online sandbox for the thesis with LatexLabs. Python code listings can be included using this trick. Overall all the pieces are in place to write it , now just need the words and pictures.