fathom - 1:39 pm on Feb 5, 2013 (gmt 0)
I was under the impression that links reported in GWT were actually approved by Google and counted as being OK. This report suggests that just because a link appears in GWT doesn't mean it's a good one.
Google merely suggests it is a private sampling of your links used to rank your domain... as a matter of disclosure if you have a problem with PENGUIN or a Manual Review involving links you can be 100% sure your problem links are included in your WMT sample.
I wish I could see a complete list of links that Google knows about that point to my site because, as with many webmasters, It's extremely hard and likely futile to build a comprehensive list ourselves.
If you had a comprehensive list you would likely have 10 times to links to sort through if you have an issue... so being careful what you wish for.