I have a need to collaborate on some complex documents and I am trying out Sphinx as the document build system. Plays nice with github, promises to play well with code (tho I haven’t really tried that out yet), uses reStructuredText for markup. I would have preferred that it used markdown (well, multimarkdown, I kind of need tables), but rST seems fine. Sphinx builds HTML, text, PDF, and a bunch of other output formats.
I also need some simple flowchart imagery and GraphViz seems like the way to go — auto generation of flowcharts, etc from simple text descriptions. Again plays nice with github, with my favorite text editor, etc.
For text editing I have moved to Sublime Text. I love bbedit but I do have the occasion to use a Windows machine and Sublime has versions for both OSX and Windows.
Oh and finally I occasionally need a more complex drawing. The Wacom Bamboo Stylus + Lekh Diagrams on the iPad seems to be a great combo. My drawing skills blow, I really like how Lekh Diagrams autocorrects my rectangles, triangles, circles, etc.