The technical term for this is "link depth origination". A search engine's crawler/bot indexes your web site (or anyone else's) only to a certain depth and then moves on to the next site. The depth a search engine crawler will go varies from engine to engine and even varies for the same engine from day to day and URL to URL. However, most crawlers go no deeper than three directory levels into any given site, like this. (yoursite.com/level-1/level-2/level-3/).
In looking at your server logs, you may find instances where a crawler has gone deeper than level 3, or shallower, but the point to take away from this is if a link to your site is on a page on the originating site that is deeper than the third directory level, the crawlers will never know the links exists. The link is deeper than the crawler crawled.
Not to mix metaphors, but imagine fishing on a lake that's 100 feet deep with a net that can be lowered only to a depth of 50 feet, and you get the picture. Anything that's deeper than 50 feet is not going to be caught by the net.
This does not mean that such links are worthless. It means only that such links cannot be factored by the engines into the engines' link popularity measurement. They can't factor what they don't know exists.
This raises an intriguing scenario. Imagine you have two sites with nearly identical content. Site A has 500 sites linking to it, but all 500 sites placed those links beyond their third directory level.
Site B has 25 sites linking to it, all of them at the highest (top) level directory.
Which site, A or B, is better positioned from a linking standpoint?
Well, it all depends. What kinds of sites do the links exist on? Those 500 links to your site will be useless if they originate on random link lists with no content and no page views, or if all those links were beyond the third directory level on the originating site. Likewise, site B with only 25 links may be getting nice new traffic if all 25 links originated close to the surface (top level) of well-trafficked, topically relevant sites.
This is an extreme scenario. It's more likely that your site falls somewhere in between. You have some good links, and you have some useless ones. You usually can't control where the originating site places its link to your site. If I have a links page that is four directories deep on my site, then even if it's the most useful links page in the world, none of the search engines are going to find it.
Let's sum all this up in a list of key points.
What is link popularity? How do you get it? In several ways, none of which are easy. There are no shortcuts to the process of building links. Eric provides credible information about the art of link building, and dispels/debunks the many claims and rumors regading link popularity, especially as it relates to search engine rankings.
Eric Ward founded the Web's first service for announcing and linking Web sites back in 1994, and he still offers those services today. His client list is a who's who of online brands. Ward is best known as the person behind the original linking campaigns for Amazon.com Books, The Link Exchange, Microsoft.com, Rodney Dangerfield, WarnerBros, The Discovery Channel, the AMA, and The Weather Channel. His services won the 1995 Tenagra Award For Internet Marketing Excellence, and he was selected as one of the Web's 100 most influential people by Websight magazine in 1997. Eric also writes the Link Building column for ClickZ, the NetSense column for Ad Age magazine, and is a 4-star speaker for iWORLD, Fawcette, and CNet.
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