The reason of all that nonsense seems to be this article: http://googlewebmastercentral.blogspot.com/2012/07/new-notif... and notifications in Google Webmaster Tools that tell people that spammy links point to their website, but do not tell them specifically which links Google does not like. I understand that Google uses link data mainly to estimate popularity of a website.
I don't understand why so large company, a global monopoly with so large revenue, and so much data gathered, can't figure out which sites are more popular than others without wasting webmasters' time. What's so difficult about that task? Why shift any work burden on website owners?
If this task is too difficult, maybe it's time to support the competition, or create a serious competition. Maybe Google does not deserve to be the largest search engine and get all the profits.