Let me get this straight - On one day alone there were about 1,400 links to your site put into Wikipedia by someone or a "bot"?
Not quite. I have somewhere near 75,000 links in Wikipedia, all put there organically, no involvement from me whatsoever. On a representative day, I got 1,400 links to my site from dozens of other sites that just copy Wikipedia onto their own domain.
Based on the 100,000 most recent links available to me in WMT, I have identified almost 400 domains that are Wiki or DMOZ scrapers. From those nearly 400 domains, I have received 67,300 links out of the 100,000, and I haven't classified them all yet. I'd estimate that of the 100,000 most recent links, 75,000 will turn out to be from Wiki cloners.
Do you really expect me to believe that Google isn't penalizing me for having 75% of my most recent links coming from spam sites? I saw a 50-80% drop in traffic precisely on 4/24, which is the sign of a Penguin penalty. Isn't it likely that 75,000 bad links will overwhelm 25,000 good links, regardless of how many of them are nofollow? Yet isn't 25,000 organic links over the course of 2 months the sign of a well-respected site, the kind that Google should be returning in search queries?
My site isn't completely knocked out of Google, but I am seeing that the only pages that can push through are those with legitimate backlinks. My thinner content pages - still the thickest on the topic on the internet though - have been eliminated from the results. My theory is that Penguin has devalued my site's authority based on all those Wiki links, and that has allowed Panda to kick in for other pages.