Footer Link Optimization for Search Engines and User Experience

Footer links may be devalued by search engines automatically
Check out the evidence - Yahoo! says they may devalue footer links, Bill Slawski uncovers patents suggesting the same and anecdotal evidence suggests Google might do this (or go further) as well. Needless to say, if you want to make sure your links are passing maximum value, it's wise to avoid the footer (particularly the footer class itself).

Footer links are often not the first link on the page to a URL
Since we know that the first link on a page is the one whose anchor text counts and footer links, while anchor text optimized, are often a second link to an already-linked-to target, they are likely not to have the desired impact.

Footer links get very low CTR
Naturally, since they're some of the least visible links on a webpage, they receive very little traffic. Thus, if algorithms like BrowseRank or other traffic metrics start to play a role in search rankings, footers are unlikely to have a positive impact.

Footer links often take a page beyond a healthy link total
Many pages that already have 80-100 links on the page are going to lose out when they add a footer with another 30-50 links embedded. The link juice passed per link will go down and the value of each individual link is lowered.

Footer links can be a time suck
The time you spend crafting the perfect link structure in the footers could be put towards more optimal link structures throughout the site's navigation and cross-linking from content, serving both users and engines better.

That's not to say I don't suggest doing a good job with your footers. Many sites, large and small, will continue to use the footer as a resource for link placement and, just as with all other SEO tactics that fade, they do carry some residual value. Let's walk through a few examples of both good and bad to get a sense for what works:

I like the organization, the clear layout, the visibility and the fact that they've distinguished (through straight HTML links vs. drop downs) which links deserve to pass link juice and ranking value. I'm also impressed that I actually see a link in the footer yet am not completely unaccepting of the idea that it could be there entirely naturally, simply as a result of what's popular.