I see two use cases for this sort of notebook thing. One is reproducible research, where I find that a woven solution is far preferable over a notebook. I can use version control to assist in iteration, and use an editor of my choice. The other is exploratory analysis, which Rmarkdown/Sweave/knitr is not really a good substitute for.

For exploratory analysis, I've found that I use the terminal integration in Vim together with the REPL works well for this. It lets me save half-working stuff and record some of my thought process; in a Jupyter notebook the only things I can leave in are working code snippets.