Dan Thies' endless seo debate with Jill Whalen about css vs. tables will never be settled without a clear demonstration of the relative merits of one or the other.
We aren't so terribly far apart, in fact, but since Ms. W insists on propounding the notion that it makes no difference where search terms appear in the content of a web page, either at the bottom or at the top, I am compelled to conduct yet another test to demonstrate this simple truth.
Whether or not an existing web site should be redesigned over this minor issue, well, I don't think it's worth spending a bunch of time and money over, because that time would be better spent on building links.
In constructing a new web site, I would use whichever layout method would prove most economical, and again, use any resources saved in a promotional campaign to build links and drive targeted traffic to my new site.