My company was hired to take over and manage example.com over a year ago. Once google updated the world and informed us via Webmaster Tools on whether or not our sites had a manual penalty or not, we discovered that example.com indeed had a partial site-wide unnatural link penalty, and rightfully so, as the site used black hat strategies years ago to grow.
Since taking over, we have worked on using white hat strategies, as well as cleaning up the backlink profile. We hired a company called [backlink removal team] who spent the last 3 months gathering ALL of the site's backlink data from many different sources and tools (webmasters, majestic, ahrefs, etc). Over the three months they made many different rounds of contact attempts to webmaster owners (not just from email data, but phone data, personal/business address data, alternative e-mail data), and were successfully able to remove ~60% of the bad links (per their software). They also mentioned that most of the time once they reach 30% removal of all bad links that Google typically is more prone to lift the penalty.
Obviously our site took a major hit during this phase.
[backlink removal team] provided us with full documentation of their every step, we disavowed the links that we couldn't remove, and we were VERY confident that Google would lift the penalty (initially we manually tried to do the backlink outreach and google responded back within one week to say that there were still more links to be cleaned up). This time with [backlink removal team], Google took 4 weeks to get back to us. In that time we assumed that they were looking deep into all of the documentation that we provided, and that it was only a matter of time before the penalty would be lifted.
Google just got back to us the other day and mentioned that there are still bad links on our site (and provided us with three links). We contacted [backlink removal team] and they said that those links were NEVER provided in ALL of the data that they gathered from every tool available.
After all of the hard work, money, and time that was spent into cleaning up the backlinks, how can Google expect us to ever get a penalty lifted when for one, we can't even FIND the remaining bad links through every tool available on the internet, and for two, they don't even provide us WITH those bad links to give us a chance to get removed?
This is simply not fair, we are a business (that gives back to teachers, parents and kids) that is struggling to survive.
[edited by: brotherhood_of_LAN at 4:13 pm (utc) on Jan 31, 2014]
[edit reason] see stickymail at top of screen regarding specifics, thanks [/edit]