I can't find a plugin that has that kind of mark-up built into it. Sounds like it could be called "Interesting Posts" or something similar, but that doesn't return anything from the Wordpress repository.

Nonetheless, the popular posts listed in the content area are generated by the same plugin that lists the popular posts in the sidebar. That can definitely be done by the Wordpress Popular Posts plugin - it lets you restrict it to a time frame (this month), use thumbnails, etc. Could very well be that they're using a plug-in like that and generated some custom mark-up and styling. It is, after all, a pretty popular site. I don't know that they'd use stuff out-of-the-box.

This plug-in is also call-able within the template, not just as a widget. So, it's as simple as inserting it in your main loop on the index page.

Inside the loop, add a counter of some kind. Increment the counter with each post. Add a check for when the counter equals your desired spot (i.e. x = 3), and then insert your div with the popular posts. Then, the loop resumes, and the rest of the posts show up in the index.

The ad and the popular posts show up in a div called "Intercept," so I thought there might be a Wordpress plug-in that automates intercepting the loop and inserting some extra content. But I couldn't find that either... seems like a simple but cool idea for a plug-in though.