anallawalla - 1:35 am on Oct 12, 2012 (gmt 0)
I believe that the algos begin with a site's reputation score, then ignore certain rules if the site is beyond reproach. For example, many sites have site-wide footer links to other sites for legit purposes, e.g. European Parliament links to some other domains not owned by it. Other sites might link to a piece of legislation that regulates their industry, etc.
The clue is in "scheme". WordPress isn't seen as commercial, so millions of instances with default sidebars and footers won't hurt WordPress (reputation also kicks in).
The probem is for smaller players e.g. one who might one day become the next WordPress but will be prevented from being found by such algos.