The article's guess is correct: I don't see any manual action on this site, but our algorithms don't think explore.to is a great site.
Jabbles is certainly right, and listen to blauwbilgorgel too--it's good feedback from typical Google users. When I clicked down randomly, I got to the category "Body Shops in Bowers, Delaware" only to see "No results were found for the search criteria you requested, we have included web search results for your query" with a link to Google's own search results: http://www.explore.to/listing/usa/de/bowers/see/auto/body-sh...
Users dislike landing on pages with no content, and they also dislike landing on search results from Google's search results--especially if it's Google's own search results.
Once you've removed the no-content pages, you still have many issues. I searched for pizza in New York and the #1 result was in Florida. That's poor quality, but even your #1 listing for pizza in New York had no original content. It was just an address, a phone number (which I had to click again to get?), and a map. Everything looked autogenerated. No reviews, images, comments, hours--anything, really.
So my advice to you would be to step back and ask yourself, "What separates explore.to from the thousands of other sites that just grab or license data from Acxiom or other yellow page data providers? Why would anyone searching on Google want to land on my pages instead of other the tens of thousands of other yellow page sites on the web?" Then concentrate on really pushing on the areas where you can add value for users.