I'm beginning to think that your sites may have been hacked and are now hosting some cloaked content (possibly links). Cloaking is the factor that makes it hard for a site owner to diagnose. It is sometimes IP cloaking rather than user-agent cloaking, and sometimes todays hacking criminals install a cookie scheme or .htaccess tricks to prevent easy discovery.
Do you have WebmasterTools set up for these sites? If so, you might see an indication in WMT. You can also use the "Fetch as googlebot" utility to diagnose a page EXACTLY as Google sees it. In addition, there is sometimes an indication that you have parasite content because funky backlinks show up en masse. Such links would have been placed by the hacker to boost their own parasite links.
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Another idea comes to mind. Google has been known to do a kind of automated "sweep" for a particular kind of ranking technique and then penalize all the sites that appear to be using that method. It is sometimes the case that a site gets "unfairly" penalized this way, like a dolphin caught in a tuna net, because of some technical similarity to the criteria Google used to build that "sweep".
Such sweeps would be designed to catch some type of violation that is described in
Google's Webmaster Guidelines [google.com] - so dedicating a chunk of time to study of all the current wording there might trip an idea for you.
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The kind of ranking drops you are describing do not sound like the result of an algo change to me, because the degree of loss is too extreme. The situation you describe has the feel of a "true" penalty to me, and a lot of the time true penalties are link related.
So I would make links - both inbound and outbound - the first point of study. Ironically, Bing may help you understand Google better, because their
"linkfromdomain:" operator [bing.com] gives you a very helpful listing about a site's outbound links.
[edited by: tedster at 6:48 pm (utc) on Mar 21, 2010]