Are Footer Links Treated Differently?
In a short answer, Yes, they do.
When someone asked Matt Cutts about it, he replied negatively. But he also indicated that the links might not carry the same editorial weight as the links in paragraphs surrounded by texts carries.
Footer Links are generally paid links or some kind of sponsor links. For example, a free wordpress template has more or less 5 links in footer. One of which should be the blog’s homepage in form of copyright notice and the other is “Powered by WordPress”. Now, one of the rest three should be the Theme’s developer’s link and the other two will be sponsored links where the sponsors paid the theme developer to put their links. Similarly, a normal html website also has the designed by on it’s footer section.
Though PR (Page Rank) flows uniformly in the links that are on the pages without regard to whether the link was at the top of the page, at the bottom of the page, in the footer or in the text. In general, Google’s link analysis continues to get more and more sophisticated as they will eventually filter out the links in the footer section and this might impact on backlinks impacting the overall SERP and PR.
