Sorry to drag this topic up again, but this issue has been an ongoing concern of mine, and I think a lot of people are dealing with this now (as the whole responsive-design thing is I think just now entering a lot of people's radars), so it would be interesting to see if anyone has any new input.
As for myself, I've had a responsive design in place on my Wordpress site for about six months. I have a sidebar on the right that gets pushed below the content at iPad size and smaller. My best-performing and most prominent ad is a 300x250 at the top of the sidebar, so it gets pushed below the content (way down below the comments) on mobile devices.
So far, I haven't concerned myself much with the ad being so low on mobile devices because I've thought of this as one of the tradeoffs for the benefits of responsive design, and also because my site is mostly a labor of love and I try not to worry about ad revenue too much.
But today I finally got around to looking into my ad stats for mobile devices, and it's a sad picture. According to Analytics, about 20 percent of my visitors are on mobile devices (and mobile users' bounce rate, time on site, etc. are roughly the same as for nonmobile users), while only three percent (!) of my Adsense revenue is from mobile visitors.
The obvious solution to this is to make it so that mobile visitors see an ad closer to the top. This seems simple enough, but there's no easy way to make it work without showing *everyone* an ad above the content, which I don't want to do. I've looked into ways to make the top-right sidebar ad appear above the content on mobile devices, but I haven't found a good way to do this. I know I can use media queries to hide the ad in one position and show it in the other depending on the width of the screen, but from what I understand (as someone who can do some CSS but is far from skilled), this causes the ad to load twice with each page load, which would lead to false impressions and potentially serious trouble with Adsense. I don't want to risk it.
I suspect I just have to take the loss while waiting for Adsense to come up with better solutions for mobile designs. But as far as I know there are no such solutions in the offing. Meanwhile, my mobile traffic is growing monthly (from 5% of the total a year ago to 20% now), so I'm not sure what to do.
Anyway, I'm not asking for solutions--just sharing my experience. I wonder if anyone else is going through anything similar.