I've read a lot of people theorizing about how Google counts some NoFollow links. I've never bought into that theory, but I've also not had any strong arguments against it.
Here's a quote from Stephan Spencer interviewing Matt Cutts that is very clear on this issue:
At least for Google, we have taken a very clear stance that those links are not even used for discovery; they are not used for PageRank; they are not used for anchor text in any way. Anybody can go and do various experiments to verify that.
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What do you think the reason for including them (no follow links) in the links shown in Webmaster tools is? Just to have in place IF big G decides they should be used for some reason in the future? If they were never going to count for anything, why show at all?
The webmaster can then see all links to his/her site, including no-follow links which could be driving traffic to the site even if they aren't passing any PR. The webmaster could also use the information to contact the sites giving the no-follow links and see if it would be possible to switch those to do-follow links.
I always had a doubt whether Googlebot considered the text attached to the link and whether it played any part in helping getting the page crawled.
Thanks for sharing Will.
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You would have to think that a site with little or no dofollow links and thousands of nofollow links is spamming in some way. The link profile is unnatural. This could be a "red flag".
I guess we'll never know because that's Google's secret.