An R package with bindings to cmark has been released to CRAN: commonmark. The package implements simple wrappers for converting markdown to html, xml, man or commonmark.
One thing we are currently looking into is adding a renderer for the Rd format to make it easier package authors for to write and maintain documentation using markdown.
Another goal is to experiment with a structure and converter specifically for NEWS.md files which are included with many R packages. In a recent discussion on the r-devel mailing list it was suggested to standardize the format of these files in a way that allows for archiving/indexing the items.
Suggestions on any of the above are welcome of course.