There are definitely good reasons to have a footer of links: providing continued navigation at the end of a long page of text without the user scrolling all the way back to the top, an alternative to javascript/flash based navigation, etc. However it is very easy to overdo this and put too many links in. The five or six most important or related pages is one thing, two lines of links might be a bit much.

An example of how this could backfire is a search for a company name. If you do a search for your company, what pages come up? Your home page is probably first, but what is next? Is it your most important product? Or is it your "contact us" page? Your contact page, for example, is naturally optimized for your business name simply by the nature of the content you would expect on a contact page. But if you include it in a footer, now every page on your site links to the contact us page, telling Google that you, as the webmaster, think the contact us page is so important visitors need access from every other page.

This used to be more of a problem about three or four years ago, in part because these sitemap footers are being used less, and I think in part because the algorithms have been tweaked to compensate for this (partially, IMHO, by a decrease in value of internal vs external links).

Basically, tread with care. You don't want to have too much there, and overload your user, and you also don't want to dilute the value of the rest of your internal links.

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