Definitely read the appendix "Tools & Implementation". He expresses frustration with the current state of the art in building visualizations.
My guess is that he is using his javascript library for "reactive documents" called Tangle http://worrydream.com/Tangle for all the demos in this article.
I'll just add that I really find this whole piece astounding and many levels above the majority of things I find on the internet.
Excellent stuff, as others have mentioned, I thought of Tufte meets Web.
The "Tools & Implementation" section had me thinking of the pure data sound programming environment - the way you drag the numerical parameters in the code (cheekily reminiscent of processing) that draws the circles to change values.
tangle.js is referenced in the html of the page, and I shall certainly be looking into that for maths visualisations at a more humble level.
My guess is that he is using his javascript library for "reactive documents" called Tangle http://worrydream.com/Tangle for all the demos in this article.
I'll just add that I really find this whole piece astounding and many levels above the majority of things I find on the internet.