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Could it not be smart to use the other link reporting tool, the one that Google itself provides in Webmaster Central?
Patrick alludes to this in the article and there was a cracking article on the blog last week (I think) on combining all three sets of data to aid link cleaning.
Yeah, I saw that when I went for a second read. I guess the headline make me think it sounded all doom and gloom, like there was nothing that could be gone when Google seems the first and best resource to be looking at.
I'd try to pull the incoming link domains from GWT and then run them through Mozscape & Majestic to check out their metrics, quality and authority. Not sure how to do this automagically though :-\.
I'm a big fan of Patrick, but I might disagree slightly that the metrics are useless. Low domain authority seems to correlate pretty well with sites that Google sends "warnings" about, so while the indices may not have 100% of the link data, the domain-level stuff is still pretty good. I'd love to see this analyzed from the root domain perspective. My guess would be that the linking root domains count between Moz, Majestic and GWMT looks considerably better (75%+, maybe even 90%+).