I wonder how many "legitimate" links a site like RapGenius gets. I've never seen anybody link to them, except maybe in social networks. Similar for the stackexchange sites. Sometimes people link to good questions from blogs, but a large portion of links are probably from other stackexchange sites, twitter, and Jeff Atwood's blog (which is a marvel of SEO and affilate marketing in itself).

For many of these high quality content silos (for lack of a better word), the PageRank paradigm seems pretty broken. People don't feel compelled to link to well-known sites precisely because they are well-ranked. And when they do, it is in form of viral posts in social networks, which is not really a great input to determine site quality.

I wouldn't be surprized if Google's real secret algorithm nowadays consists of millions of special cases maintained by thousands of poorly paid interns.