I've often thought about how the position of a link on a webpage can affect its ability to pass trust and PageRank. We've all seem websites which have horrible looking footers or headers which seem to be stuffed with useless links to bad quality external websites or internal pages which are being targeted with keywords. The way these links are presented isn't always very helpful to the user, if this is the case, then it would make sense that Google gives less value to these links than they would to links right in the middle of the page or in the middle of content.
In his latest Google Webmaster Video, Matt Cutts confirms this and explains how Google are getting smarter at evaluating the value of a link based on its position on the page.
I still think that footer links can pass value, however they need to be presented in a way that is useful to the user. Many people will often scroll to the bottom of the page after reading an article and wonder where to go next. If there is a nice navigation menu in the page footer with some useful links then I can't see whats wrong with that. However if its a footer stuff with 50 links in small text that is hard to read, let alone click on, I can see how Google would de-value those links.