One thing that would explain how some sites, like eBay, now dominate serps for many product keywords would be a sudden change in how nofollow is handled.
Hi there, Sgt_KickAxe:
I think you may have posted a similar question a few weeks back about this (I apologize in advance if I am mistaken).
I think that even if no-follow were ignored for sites with high authority (ebay, amazon, etc.,) I think that google would still treat them as "affiliate" links and would hopefully not flow page rank through them.
But maybe those no-follow affiliate links are not (technically) part of Page Rank, but instead add to "authority," which in turn helps with ranking?