Those have recently started to increase in frequency, not because people are doing it more or Google is penalizing sites more for it - but only because Google is now communicating about those cases more often.
That being said, if you respond to one of those messages via a reconsideration request, Google may give you specific examples of which URLs are pointing to your site that they find to be "inorganic" and "unnatural." Typically, the information is not included in the first message but on follow up a human Googler might give some specific examples if they feel it might help in this case.
Google will sometimes reply saying something like:
There are still many inorganic links pointing to your site. Here are some examples:
Again, this is Google being more transparent about things. And if you did get this message, it doesn't mean you were penalized that day, especially since Google has stepped up communicating on this topic. You could have been suffering from this for a while before. And don't confuse this with the BuildMyRank case.
Forum discussion at SEOmoz Q&A.