A thread at WebmasterWorld speculates about how Google is weighing factors throughout the site rather than on a single page on a domain.
Some people are seeing that Google is placing heavier emphasis on so-called "landing pages" that might bring people to the appropriate content.
Some are seeing a strange trend toward SERPs that rank higher level pages that are actually one click away from the real "meat"
Some members see that there is an emphasis on overall site relevancy:
... the changes trigger an effect that you describe, because of (forcing) relevant site navigation....
If the internal navigation is meant to combine or further develop this relevancy, no matter what page the links and visitors land on, both the users and the algo will gladly admit that on a widgets page ( page, not site ) the internal links promote other pages to be of value about the keyword "widgets" even if the anchor of the internal navigation doesn't mention widgets all over again.
Other WebmasterWorld members are cautious to approach this purported algorithmic change, especially because Wikipedia is more-or-less a site that does not focus on any specific theme and is "disconnected" in terms of site-wide relevant content:
I see no evidence that Google is looking at sites rather than pages; it's just a weird coincidence that pages in the same site are often linked :) and so each may benefit from it's neighbor.
As personalized search continues to creep up into our world, speculation revolves around putting heavier emphasis on user behavior as observed from the Google Toolbar:
G will start looking at all their data acquired from the G Desktop & Toolbar stats to determine the quality of a "Site", and place some sort of unknown, unseen score, like PR, but based on how often users bounce back off of it, bookmark it, or time spend cruising site, or number of pages surfed, or some combination of all of the above. This will then be used somehow in the Algo to boost the trust rank, floating the quality to the top, & the crap that no-one wants to see to the bottom.
Are you noticing anything different in the search results that might show that Google is emphasizing the importance of the entire site versus a single factor?
Further speculation, including responses to a recent statement by Matt Cutts, continues at WebmasterWorld.