MikeNoLastName - 12:07 am on Jun 23, 2012 (gmt 0)
The Question is "do they" and "how do they" determine onsite and inter-site backlinks. Numerous sites have consistent navigation menus with the same major keywords across the top or side of EVERY page. This should be a good thing for "usability", no? Is it penalized?
Now lets take that a step further and say your website is spread across 2 or 3 domains, all of the pages on all domains have the same menu which links to pages on each of the domains, because the title of the site is the same on all 3 domains and each domain contains an integral part of the big-picture site. Can they recognize it as the same owner and all being the same or similar topic and thus one "big site" and thus NOT un-natural linking at all? (I doubt it). Alexa BTW has an option for interlinking the reports, but as far as I can tell GWMTs does not, other than the fact that you can add multiple domains under the same account, but there is no way to confirm that they look at this info when ranking.
Finally on top of all that, say you are getting 2 or 3 external dime-a-dozen type sites, unknown to you, and they love your reference page so much because they are too honest to scrape it and too lazy to create their own, that they link it from the template (i.e. reproduced exactly) side bar menu of their 1000's of rambling blog pages on topics barely or not at all related to YOUR site. I agree it probably shouldn't count for much, but this should not be penalized either.
I'm sure there are more examples of things that G probably has not bothered to think about in unnatural-inter-linking of sites.