I agree to a point on this one. Organization plays a major role with a site and its contents. But then, a dictionary is also very well organized, but you wouldn't put that at the bottom of your site, right? When you're talking a lot of links, no matter how organized it is, it's going to be ugly.
My company has put up links like this to the geographic locations we service two times, and both times they've taken them down. I'm not saying there's no SEO benefit to having a site on the home page (top, bottom, wherever). What concerns me is that now the needs of the user are playing second fiddle to the spiders.
I propose the following analogy: a site is like a Christmas tree and users love to get in all the branches and see where they lead (okay, work with me here). The thicker the trunk the more sturdy the tree will be (aka a stronger site). What about the spiders? Ahhh, they're attracted to the nice shiny ornaments that are on the tree, but they only come after the tree is fit to be decorated.
If you have too many ornaments, the tree looks gaudy and the tree doesn't look so strong anymore. The line separating the user's needs and the spider's needs has been broken, and things have gotten messy.
Okay, kind of weird mixing spiders and Christmas trees, but hopefully you get my point.