There seems to be some evidence that placing links within naturally written sentences is more effective for passing on juice (as opposed to footers or sidebars), so if you can do that in a way that works for your visitors, you may see better results.
Google may filter out what it thinks are “part of the template”. The footer’s a bit obvious as “Part of the template”.
Matt Cutts mentioned that this was going to happen in Las Vegas after the search engine smackdown, he said it was going to deal with websites with “spammy footers”