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I was surprised to see those links show up in the GWT "Pages with external links" list.
On About rel="nofollow" - Webmasters/Site owners Help [google.com] it says
How does Google handle nofollowed links?
We don't follow them. This means that Google does not transfer PageRank or anchor text across these links. Essentially, using nofollow causes us to drop the target links from our overall graph of the web.
Now why are they showing up in GWT in that case? Surely Google has a practical interest in those links, at the very least to see what the anchor text says!
[edited by: gsmith at 2:44 am (utc) on April 22, 2009]
If you test that kind of link, I'm confident you will find that anchor text influence is indeed not being passed.
When you think about it, so long as their robots are coming across those links why shouldn't they analyze the data? I understand why they don't want to give weight to nofollow links when calculating relative ranks, but why not analyze the text for one reason or another?
The first reason that nofollow was created was for social media sites to protect themselve from spammers. It is relatively simple to script a bot to place spam links all over the blogs, and that practice was rampant. Then there's the practice of "Google bowling" where automated posting of spammy links attempts to knock the rankings of legitimate sites around. That needed some protection, too.
Having created the nofollow attribute to protect webmasters, Google will not go back now and analyze the data for use in their search results - neither for query-dependent factors such as anchor text, nor query-independent factors such as trust or PageRank.
Do they keep stats on rel="nofollow" links, just privately held data? I'm sure they do. Even in the video, Matt mentions that nofollowed links make up a very small percentage of all links on the web. So they watch it, and they know about it - they just don't evaluate urls based on it. Google doesn't even use nofollow links for url discovery.