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).
[1] https://github.com/ipython/ipython/tree/master/IPython/nbcon...