@ Sgt_Kickaxe:
Could it be as simple as ignoring nofollow to sites Google trusts?
I can't give you any real information, but I keep my ears open to a lot of link building gossip, and I am always happy to pass along gossip.
I haven't heard anything on the linking forums out there about nofollowed links passing value to "trusted" sites.
I have heard a lot of people say publicly that they think the role of link-less citations (just mentioning the URL without linking to it) seems to be gaining in importance in ranking.
Now, these are on public forums, and the people who say that may, or may not, be talking out their caboose. I would just say that there is a lot of talk about it. And, I am sure there are TONS of people who cite big name sites like amazon, ebay, zappos, etc, that don't actually link to them. So that might hold water.
another thing to think about in the case of amazon in particular is that they sell books by university professors, and you will see (non-affiliate) links to those books from the professors' pages, which are hosted on high PR / high authority sites.
so I would say there is a significant amount of "straight" links from university sites to amazon pages, since the professors are NOT interested in spending their time becoming amazon affiliates (but they ARE interested in spending their time promoting their books).
Unfortunately, I have no stats whatsoever for the ratio of "straight" links to affiliate links from university professor pages.
Another thing that others have alluded to on these forums is that aside from measuring click through rates in the google serps, google most certainly is measuring when people type in a URl directly in either chrome or android. And lots more people are typing in ebay.com and amazon.com and zappos.com than are typing in MyLongTailKeywwordStuffedUrl.com
anyway, these are all just guesses at what could possibly be happening.