Google and Bing have been using page segmentation to differently weight different sections of a page for a number of years. Many web people I speak with believe that internal links in certain "blocks" such as a blog roll or the footer most probably* are substantially ignored.
See Bill Slawski's Google's Page Segmentation Patent Granted [seobythesea.com]
How a Search Engine Might Identify the Functions of Blocks in Web Pages to Improve Search Results [seobythesea.com]
And if you think about it, if a footer link to the home page were to be somehow "penalized" then just about every site on the web would be wiped out. ;-)
*And, of course, we don't know, we can only say most probably.