Google and Yahoo say they count multiple links from a site once. Actually, their exact words to me were “diminishing returns”, which I took to mean that maybe you get a stronger link, but it is still one link. They did elaborate and say that the strongest link from the site will get counted as the one, mostly this will be the homepage of a site … for instance, some of the older posts on CAP that have received links from other sites will get more link love than the random post that no-one cares about.