Most significant link building factor
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Am I right in thinking the most important link building factor is the number of unique linking root domains? Multiple links from a domain won't help me so much?
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I would say (more importantly) the weight of those links (not the necessary number). Multiple links will help from one site, but the value is probably greatly diminished unless those pages are popular (or have a high 'pagerank').
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This should help you:
http://www.seomoz.org/blog/10-illustrations-on-search-engines-valuation-of-links
All things being equal, more domains is better than more links. But, I agree with Kevin, it really depends on the trust and authority of the domains. Two links from an authoritative and trusted site are going to be worth a 100 low value domains, perhaps more.
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Always remember that "relevancy" is a vital part of unique linking root domains.
If you have 1,000 links on 1,000 different "car" related domains, you might find it hard to rank your "pets" website.
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I don't think relevancy is crucial. a car site could be linking to your pets site because you sell pet carrying cases for traveling with your pet. It's too difficult for Google to definitely determine relevancy and discount the value of a link. Of course you don't want all links from sites that have nothing to do with your niche!
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It's true that number of unique linking root domains is important. It's true that multiple links from a domain won't help as much as links from new domains.
But there are a ton of metrics that matter - relevance, trust, authority, anchor text, etc. So I'm not sure "unique linking root domains" is the single most important factor. It's definitely important, though, and correlates well with Google rankings: http://www.seomoz.org/blog/announcing-the-march-mozscape-index
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Am I right in thinking the most important link building factor is the number of unique linking root domains?
One link from the Pope's site will be worth 10,000 links from spam blogs.
Multiple links from a domain won't help me so much?
Again, it depends upon the domain. But, if you have multiple links from a very high quality site it will benefit you more than one link from that site. And, if those links hit multiple pages on your site then each of those pages will get measurable benefit... and that benefit, I believe, will flow through your entire site.