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Agree on most of the pointers/facts listed on this post.
I actually experienced recovering from a manual penalty first hand - on my blog, which happened 2 months ago (unnatural link warning sent on May 23 - and the manual penalty was revoked last June 14).
Well there were 2 reasons why I got the manual penalty:
1. My blog was a victim of a negative SEO campaign last June 2012 (but I was able to disavow all of those links way even before I received the Unnatural link warning, I believe I've disavowed those links as soon as the disavow tool became available).
2. I realized the second reason when I failed on my first reconsideration request. I remembered that I did a case study on exact match anchor texts on reciprocal links 2 years ago (yep, deadly sitewide links from 4 topically relevant sites).
Although I didn't really remove these reciprocal links (since these are mostly from industry peers), I just asked them to change the anchor texts (into a branded one). Then submitted a second reconsideration request, then the site was reconsidered after 2 days :)
Well, that's actually the fastest recovery I've encountered so far (as for some of our new clients, it took weeks/months to remove, disavow and get reconsidered).
So my point is, if you're really confident that you haven't done anything wrong to violate Google's terms, then there's nothing much to worry about. Just be really honest with your copy for your reconsideration request (and make it as succinct as you can).
7 months, 3 weeks ago on Google’s Manual Penalty > Why You’re Still Doing it Wrong