Most SEOs know that sites, as a whole, can eventually lose their trust from Google to pass link juice and PageRank. Sometimes this is done on a sitewide basis and sometimes it is done at a more granular level. It is probably also done both on a manual action basis as well as on the algorithmic basis.

John Mueller from Google made a comment about it at the 5:35 minute mark into a Google+ hangout from late last week.

John said:

Here is the video embed at the start time:

Then Daniel Picken asked on top of that, “would affiliates and directories fall into the category of not passing any PageRank?” Which John Mueller replied, “not by design, no.”

Forum discussion at Google+.