It all depends on your average speed. Aerodynamic drag is proportional to the square of velocity, so doubling speed from the 50km/h city limit to a 100km/h highway velocity quadruples the energy wasted on open windows. On the other hand, A/C imposes a fairly constant power draw, which is a greater proportion of your fuel consumption at lower speeds. So as a general rule of thumb, drive with the windows down inside cities and use the A/C in highways.

As far as quantitative studies go, the results are mixed, depending on the type of car used. While [1] is claiming a 35% efficiency loss for driving with the windows down, compared to a general 15% eficciency loss for using the A/C, [2], that used a semi instead of a compact car, found that windows down was actually better than the A/C by 9.5%, at 65mph.

My own take at on the matter is that you're better off doing your own tests. Furthermore, for me, noise (urban noise as well as aerodynamic noise) is an equally important factor when I decide to close my windows and use the A/C.

[1] http://www.gasaddict.ca/casestudies/FuelSmartCaseStudies.pdf
[2] http://www.edmunds.com/advice/fueleconomy/articles/125158/article.html#aero