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A lot of things come into play but I reckon you are using so called GURU tools Seomoz or MajesticSEO and such. Smart kids that get good links they get the sites to block those 2 crawlers from tracking.
If only Google could fix their damn algorithm to ensure that the homepage actually stays in the index at the weekends as well as on weekdays!
Now you could scan the backlinks of a great site and just find junk, but the real links are far better and they are just hiding it.