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"Linking root domains" is a metric we use because it correlates better with ranking than your overall link count. In other words, if you have 100 links from todd.com (even on different, non-root URLs), that counts a lot less for SEO than having links from 100 different root domains. It doesn't necessarily matter where the link is from the home-page or a deep page (home pages tend to have higher PR, but just on average). What we're really interested in is how many different/unique domains link to your site.