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Because the other sites were banned I can only deduce it was via similarities in the IP ( same class but not same IP), dns or registrar. There is no other explanation because some sites are totally unrelated.
How our company works is that we buy domains centrally, get the admin to set it up on one of a few servers and then let our guys get on with building different sites. I always wondered if it was a bit too lazy and now it seems it was but as we recentley spent 14,000 USD on server hardware we did not want to go to virtual hosting elsewhere after buying that kit.
I feel really sorry for the guys who have been hit with a penalty because they are guilty by association with our "dirty" hosting.
Are you talking about a penalty (lower ranking) or a ban (not in the index)?
I would assume that it's the common ownership (registrar information) that's creating the problem. But even then, there is probably something on at least one of the sites that Google considers a major violation. Thin pages don't get ranked, but the site isn't banned. That takes something more spammy, like dodgy backlink schemes.
I can't say for sure, but I do know that when Matt uses his tools at site review panels, he comes up with some wildly accurate stuff very quickly.
A dodgy backlink scheme plus common ownership - yes, I can see that happening
Not only dodgy - a repetitive link scheme to all domains - even with very editorial links - over numerous websites that are on the same C class can do this as well.
In my estimation its about patterns - some are acceptable, and others cause domains to cross thresholds. When they are detectable relationships with other domains, the other domains take the fall as well.
Tough to say whether protected whois is information that Google has and / or uses. My sense is that there are likely other patterns at work here which are sufficient enough for Google to trace without needing to use protected whois info.
This all comes back to thoroughly researching the network, how it is developed, registered, and linked to at start-up.
So I think the tools that Matt and his spam team have can sometimes take down people with similar data. Well nothing is perfect. Perhaps they could add a quality score to double decide if a site on the neighbourhood should be taken out or not.