First up, and probably of more interest to most people, I've begun the documentation for the MathML definitions used by Names on Nodes. The document includes general reviews of relevant mathematical and biological concepts, a quick review of MathML and the technologies it's based on, some comments on correlating mathematical and biological concepts, and definitions for all entities (including operations) used by Names on Nodes. Note that this covers a lot of the same ground as in my 2007 paper, with a few minor changes in the symbols and terminology (e.g., I now call the ancestor of a clade a "cladogen" rather than a "cladogenetic set").
Secondly, I've made the project open-source, by moving it to Google Code. If you are a developer interested in checking this out, go here. It's incomplete, so I don't know if anyone will have any real interest in looking at it yet. (Honestly, I mostly posted so that, on the off chance that I unexpectedly kick the bucket, my magnum opus won't be lost forever.)