I work with Doug Pierce, who is mentioned in the article. If any HNers have any questions about this story, I'm happy to answer the ones I can and pass on any that I can't.
I actually figured out what the basic strategy was, but Doug dug up a ton of data on exactly what they were buying. Some of it is kind of insidery stuff you'd want to know if you were an SEO but not if you were a typical Times reader. (David Segal does a really impressive job in general of writing about this stuff in a way that's understandable to the average person. I hope he does an article about white hat SEO some time, so I can cite it when I explain SEO to my clients.)