More and more I see sites that are using inbound links in the footer. The idea of creating a list of inbound links is a great idea (you can help distribute page strength) but it's become increasingly clear that the footer is no longer the place to keep them.
Search Engines might devalue Footer links
An interview with Yahoo's Priyank Garg reveals they might devalue footer links. There is also speculation that Google might penalize sites for too many Footer links. Not to mention numerous reports from webmasters (including myself) that they have seen a jump in rankings when inbound footer links are removed.
Footer links have terrible CTR.
While I doubt that webmasters place inbound links in their footer in the hopes of directing traffic, the truth is, nobody clicks on them. Consistently we've seen that footer links are almost never used by visitors.
Footer links can lead to unhealthy link totals
The amount of juice passed by a link is affected by the number of links on a page. Many sites have dozens of links per page and adding more links in the footer can negatively affect the strength gained from each link. This is also something to keep in mind when evaluating the value of a link in general - try to stay away from pages with over 100 outbound links.
Use 'nofollow" links instead
If you must use links in your footer, think about using some "nofollow" links. I'm sure there are some pages on your website that you wouldn't want gaining in page strength (policy pages, forms, etc.). "nofollow" links are not recognized by search engines and thus wont negatively affect your page or link strength.
Make functional Footers
Don't just stuff links into the footer of your website. Make them look attractive and provide a functional purpose. There's nothing worse than seeing a footer jumbled with inconsequential links. Try placing relevant links in your footer, or separate them into categories, your visitors will be much more inclined to use them.
This is a very common mistake perpetrated widely throughout the online community. Footers might provide functional aspects for larger websites but most websites simply don't need them. Additionally, the fact that search engines might devalue these links might convince webmasters to stray from this practice.