I had 3 of my sites in a -50, these were my first websites and I had no clue what I was doing and so I engaged in various crappy link building tactics, crappy directory links, bought a couple of links, used recip link pages both on site and got them from other sites on their link pages, used crap blog networks, article marketing on turbo, getting tons of links from one identical article distributed to thousands of sites and the like.
Also, not knowing anything at the time, I got links in excessive rates, in one month I had gotten over 1000 links and most ALL externals were to the home page, barely any internal page links at all, nor very little variations of anchor text, so the link profile looked very manual and unnatural.
Symptoms at Time of Penalties
1. Everyone of these sites was page 5 or 6 for the tld without .com, so for example, bluewidgets was page 5 or 6, and these domain names were not common.
2. All 3 sites were ranking Page 1 (Google) for some time for their sitewide kw's, home page and several inner pages when penalty came.
3. Bing and Yahoo ranks not affected, ranked for several terms.
4. Once penalty hit, ALL kw terms, especially the home page/sitewide kws would not move past page 5, mostly jumped around pg 5 - 6.
5. PR had not changed for any of the sites, 2 were PR3 and the other PR2, then and now.
What I did initially:
1. I got rid of all on-site crap, recip links pages, overdone internal links, footer link to home page with keywords, most all home page links on the site that had sitewide anchor.
2. Also a couple of these sites interlinked and so I set those links to nofollow, eventually I deleted them all together. (these sites are same IP)
3. I could not get rid of most of the external crap links, but I got rid of a few.
4. One of the sites was a blog, so I got rid of most of the blogroll, just kept a few good recip links.
5. Added some fresh unique content, (which all these sites all ready had) but I added more.
6. Then I left them alone, stopped building links of any kind, but kept adding content to all of them.
These penalties happened in late 2008 and just 2 weeks ago, around June 5, 2011 one site recovered on its own.
1. Initially when penalty lifted the home page of this site was on page 1 for main site wide kw's (2 of them) for about 2 weeks, now fallen to pg 8 or so, of course due to not having any fresh quality links.
2. Ranks #1 for tld without .com
3. Inner pages jumping, around pg 2, 3, 11, 8.
So, in my case it took over 2.5 years for the penalty to lift on its own, the other 2 sites still penalized.
In my case the only explanation was crappy backlinks, and lots of them.
On site SEO I do not think was as significant, all though the useless recip links pages might have had some impact, but I still see site after site with 4-6 pages of recip links and not penalized, so, I believe that in main part crappy links, ineffective manual link building and overall unnatural link profiles were the culprit for this penalty, in my case anyway.
I never asked for reconsideration, at the time I had no clue why it happened or what I did, it's only now that I have experience that I understand the whole picture much better, so I really had nothing to say to Google.
I hope this helps someone, the news is not great I know, ie: 2.5 years