tedster - 4:45 am on Mar 11, 2011 (gmt 0)
Along these lines, I recently analyzed backlinks for a business that runs two domains - example.com and exampleblog.com. Google acknowledges only the links between those two domains, but in reality they have about 800,000 paid dofollow links.
All those links are obviously an ad buy when you visit the pages. Very clear example to me of Google just saying "we know they're all ads, we'll just nofollow them in our own webgraph.
When I analyze backlinks, I also prefer looking at linking domains and not total links most of the time. It seems that run-of-site links, even in a blogroll, are counted only as a smidge more than a single in-content link at best.