I have mentioned previously about our -50 penalty but I'm gathering some fascinating information, It's a long story though!
We are experiencing the same -50 penalty across a significant number of domains, it manifests as a wall we cannot pass for any keyword around page 4-5 depending on the keyword, in our case it was triggered after an accidental follow link back to our corporate domain was added to a number of subpages on different domains.
So far we are 100+ days plus into this penalty, the offending link was removed as soon as it was noticed, it is affecting both domains with 0 backlinks and domains with natural aged backlink profiles of hundreds of links (both which previously ranked) so in our case it isn't a suspicious external backlink profile, and it definitely isn't an over optimization penalty as all keywords are affected. These are the two reasons I generally hear for -50 penalties
We've done a lot more digging into it. Fixing the initial follow link problem that caused the penalty didn't help us at all, even after waiting 90 days, so something else is wrong or else the original crosslink offense is deemed so terrible that it's worse than the 90 day blackhat penalty attributed to JC Penney....... We have had no notifications of the penalties from Google via Webmaster tools or any other notification method, although in a particularly ironic turn we do appear to be getting rather more Adwords invitations than we've ever had before!
One of the most interesting parts of this relates to Google Analytics. We use Google Analytics on our sites, and every site of this style in our Google Analytics account is affected, without fail (NO EXCEPTION). We have a number of sites not in Google Analytics these were left out accidentally, they are the only domains of this style that rank normally, no penalty has been applied to them at all. They have even gained a few positions! (There is no difference to these sites except lack of GA code).
Also interesting is the way these penalties were applied, domain starting with the letters a-m were penalized first, then exactly three weeks later (Sunday Night) the domains starting n-z were penalized, again without exception. these domains aren't found anywhere on listed with a a-m n-z split.
These two factors make us think that we have been manually reviewed both in the time taken to look through all domains and the face that someone has noticed we use the same Google Analytics ID and used that to grab a list. As mentioned earlier we have no notifications of any kind in Webmaster Tools as to the reasons for the penalty - sites that were formerly superb search results (and held no1 position for up to 3 years prior and with better metrics than any of the competition in terms of bounce and pages viewed).
So, my current working theory is that the initial detection of the crosslink caused us to be put into manual review, someone from google has then looked at one or a few of our sites and taken a dislike to them, applying a penalty. They most likely determined that these sites are a thin affiliate, or "cookie-cutter" then then used the Google affiliate ID to identify the other sites and slapped a -50 penalty on them all. This is also corroborated by the fact that other sites that we run with alot more content on them (and arguably a "brand"), but utilize the same affiliate model survived without penalty despite being in the penalized Google Analytics account.
So as a approximate sum up of the Timeline:
Day 1 - Add Follow Link to corporate site from subpages
Day 5 - Notice -50 penalty across all domain a-m
Day 6 - Identified and removed Follow Link to corporate site from subpages
Day 26 - Notice -50 penalty across n-z
Day 110 - Still no recovery
Other interesting tests we have done:
Adding Google Analytics code to site that survived due to it initially being missed off. The sites "jumps" around up and down a few positions for a few days after the analytics code is added, but still remain unpenalized 80 days later (This indicates to me that the penalization was a one off event)
Completely changing site, moving server, CMS, but keeping the same domain: The site remain penalized even with complete recode from ground up and no affiliate link anywhere on site, even 100+ days later.
Redirecting penalized domain to new domain: New site unpenalized, and ranks as well as previous site did for it's keywords (so implies to me that penalty isn't passed, but link power is!)
Moving site from www.domain.com to a subdomain (penalty remains)
So would be great to discuss this, I have plenty of data so feel free to ask questions. The normal solution to this type of problem is to file a reconsideration request, but that's not practical as I have a lot of sites with the same issue.