I'd suggest you check out the Geo Vista site and their software. The Visual Inquiry Toolkit, provides a GUI program to implement the bi-variate chloropleth maps (I know one poster on here works at that project and may be able to point to other resources).
I think the cartogrammer blog post is sufficient to explain the technique, but here is a pretty cool article (open to the public) to see its use in practice.
Geovisual analytics to enhance spatial scan statistic interpretation: an analysis of U.S. cervical cancer mortality
Jin Chen , Robert E Roth , Adam T Naito , Eugene J Lengerich and Alan M MacEachren International Journal of Health Geographics 2008, 7:57
I hope to see some code examples for Python and R too! Basically any program that can implement a two-scale color scheme (or bivariate) can create a value by alpha map. Although all of the implementations I have seen listed so far are for choropleth maps, there is no reason you couldn't implement this for a raster or point based map as well.
I've recently written a blog post about how to implement them in ArcGIS, Making value by alpha maps with ArcMap. It basically entails making separate layers for a given transparency, and then utilizing the vector editing tools available within ArcMap to produce the necessary bivariate legend (or using a fake inset map to replicate the legend if you want to produce a black background VBA map).