Is the list of links for a site shown in Google Webmaster Tools a complete list or just a sample? I've noticed that the links in there appear to be all the ones I didn't think would have any real value - either because they were nofollow or from irrelivant sites. The few I did think would be some use have never shown up and there's also some links that are sometimes there and sometimes not (such as my linkedIn profile). Does this mean that the missing links don't/no longer carry any value?

It almost appears that the list is there for Google to either inform you about problems (there was a useful list there when someone tried to SPAM my site) or mis-imform you about which link-building strategies work or not (to keep people guessing about what works or not).

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No Google does not show all links in Webmasters. See this: https://www.google.com/support/webmasters/bin/answer.py?answer=55281&hl=en

Not all links to your site may be listed. This is normal.

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