I haven't started meaningfully playing with nbconvert yet, but I think one of the really promising features are the nbconvert templates[1]. From what I gather you can make custom templates with jinja and invoke them on the command line. It would be interesting to create a docbook, msword, specifically formatted pdf templates which would allow IPython Notebooks to flow into existing print publication workflows (if I recall O'Reilly uses docbook, yes?). I haven't been able to find documentation about the nbconvert templates so I'm dragging this out of memory from an email or a tweet I saw once upon a time.
One thing I'm hoping to figure out is a way to transform IPython Notebooks into PDFs that satisfy my university's dissertation formatting guidelines (one inch margins, 12pt times, etc).
Wow, you definitely have some great ideas here, and given the enthusiasm about ipynb, I would not be surprised to see these things happen in the next 6-12 months.
O'Reilly does use docbook internally as part of the toolchain, but asciidoc is coming into style as well. I've done most of my work in docbook with a docbook editor, but did some of my latest boook in asciidoc, which was much easier. Just use a standard text editor of choice (like Vim) and get right to it. Much easier for me, anyway.
One thing I'd really like to see is ipynb supporting asciidoc instead of or in addition to markdown. You can go to/from asciidoc and docbook in a lossless way, IIRC.
asciidoc support would require an ansciidoc renderer written in javascript, which does seem to exist[1](although I haven't used it). This also highlights some of the problems with markdown because it is an insufficiently rich language for generating semantically meaningful markup for use-cases beyond blogging. There has been some really interesting work on "scholarly markdown"[2][3], but given the social and technical complexities of markdown implementations and the community[4] seems like adding asciidoc is easier than fixing markdown.
What an awesome idea -- I can think of some sociologists/biologists who had to suffer through MS Word equation editor with excel charts who would love something like this. The internal hyperlinks would be awesome too.
For now, at least you can "decode" ipynb to LaTeX and use the %%latex magic.
I would also love to see a publishing workflow that could render IPython Notebooks for print on dead trees.