Regarding various theories above:
-- We have three sites that dropped out simultaneously on 6/27/06.
-- They've been on-line since 1998, 1998, and 2001.
-- PR5, PR5, and PR4. No artificial PR inflation.
-- Only 5 advertising-based inbound links total ever rented, and removed when Google/Cutts made it clear they didn't like this promotion method (since they weren't marked with rel="nofollow" attribute). Link source sites were relevant to theme.
-- Pure white hat, always.
-- Two sites nearly all unique content, and one site 60-70% unique content (good content, we purchased site on 1/1/06 and are working to rewrite).
-- Never any sp@mmy old-time SEO tactics, like hidden text, keyword stuffing, high keyword density, etc.
-- Constantly add at least 3 new unique articles per week.
-- All site content tightly-themed.
-- Some relevant visitor-useful internal cross-linking.
-- Canonical non-www/www .htaccess/Mod_Rewrite in place about six months. Google SERPs looked good.
-- Clean .htaccess file, redirecting all known 404s to proper locations.
-- Clean, small, accurate, validated robots.txt files on all domains.
-- Hundreds of relevant "real/quality" inbound links from sites in the theme/topic gathered over the years; only a handful of reciprocal links.
-- Proper tiered organization by topic and good PR flow.
-- No broken links, internal or external.
-- No dead end pages.
-- Non-sp@mmy visitor-useful Title tags and Meta Name Description tags. No Meta Name Keywords tags (seems to us they rarely/never help, but *can* hurt.)
-- None of the sites cross-link with any others, and no external site-wide links.
-- All external links carefully checked for multiple quality factors.
-- No subdomains whatsoever.
-- Sites page counts are 750, 800, and 1700; all added naturally over many years.
-- One relevant affiliate link on most of the pages of one domain, one relevant affiliate link on one half of the pages on one domain, and only a handful of relevant affiliate links (mostly, amazon.com book links) on one domain.
-- Hosted on our dedicated web server, owned by our 5 year old hosting company. All domains are quality. These three appear to be the only domains--of about 105 domains--that went down to June 27th, 2006 ("A Date Which Will Live in Infamy").
-- The three domains represented an average 12-15K unique visitors per day, with thousands of solid rankings.
-- I see no logic in Google applying a filter or penalty that:
a.) Removed the index/default/home page from the site: command;
b.) In the site: command SERPs replaced all text snippets under the tile with the Meta Name Description;
c.) Jumbled the site: command SERPs results so there is no page priority;
d.) Left all of the Google Site Maps analytical data on the site intact;
e.) Did not use the Google Site Maps interface to notify "real/good" of the problem so they can correct and enter a re-inclusion request.
These sites have been nurtured over the years to be 100% in alignment with Google's Webmaster Guidelines. We trusted that doing so would firewall us from just this kind of drop out. We're currently running at 10% of traffic.
I've been building sites and engaging in conservative SEO/SEM since 1995. Sure, I sometimes still make stupid mistakes and will always have a lot to learn, but I can see NO reason any of these three would do anything but be fully crawled, fully indexed, receive good rankings on our targeted medium and long tail searches, and receive solid traffic.
Google intentionally penalizing/filtering/banning these three sites at the same time and giving priority to sites that are currently occupying our previous ranking spots...I don't think so...