When this trend spreads (and I say "when", not "if"), this will be a tax on the utility of the web that must be counterbalanced by the utility of the intervening pages...If they are purely designed to capture additional clicks, they will be a degradation of the web's fundamental currency...
The typical self-linking strategy involves a site creating one or more "topic pages" that consist pretty much entirely of other articles related to that content. Most of the time the links on the topic page link to proprietary content of the site owner, not to the web in general. For example, this is the NY Times content page on Russia.
If you look closely at it, there's a couple of links to third party sites, but the prominent links are NYTimes pages. Note the search engine friendly nature of the URL: http://topics.nytimes.com/top/news/international/countriesandterritories/russia/index.html
Having spent 5 years at Topix, the creation of topic pages is nothing new to Marksonland. We launched with 150,000 of them in 2004 and now the site has over 500,000 such pages. When we first launched, all the links on the topic pages went to 3rd party sites that we crawled - now many point to proprietary forums or licensed content.
So what's the magic in the creation of topic pages? Well, first it does allow you to crank up page views for your site users. All internal links do that though. The real magic is in the SEO though. The site owner gets to create dynamic content on static URL's that are optimized to popular search terms. With any of these urls, you can apply some SEO magic to them and, voila, your site actually comes up as a result for searches that are really just tangentially related.
O'Reilly mentions Crunchbase in his article, and rightly so. Arrington does a good job of self linking. Here's the search for Twitter, Blekko and Anna Patterson (Cuil's founder). There's a Crunchbase result on every page. Whether or not those results are good results, well, that's an editorial judgment. From Arrington's point of view - and from the NY Times, Topix and everyone else who does this point of view - he's now competing for traffic on search result pages that he otherwise wouldn't be.
Here's an example of the NY Times topic page showing up as a search result on one of their competitors (Gannett). A bit more SEO magic and maybe it ends up showing higher than the primary entity!
Anyway, as the Web continues to grow and more and more site traffic becomes referral traffic from Google, the creation of pages that are easily index-able by Google becomes more and more important. And so does the job of search engine discovery (SEO) of those pages. So, yes, there is no doubt this trend will continue. Perhaps not to the benefit of the web in general, however.