I found this article interesting, i got sidetracked with looking for your site, matt.
it deals with wind drag versus leaving the air conditioner on. however, in my opinion (i always have something to complain about i guess) that it doesn't deal enough with different types of cars enough. i know our passat is curved around the windows, and when they are down they "scoop" the air in terribly. but my rabbit has its windows parallel to the line of travel of the car, so it doesn't scoop any air unless you have one of the vent wing windows open.
I've read a lot about it and came up on my own that a low speeds you should have the windows down and at high speeds the a/c on, I'm not sure though. It would be interesting to try for sure. In any case, I drive windows up no a.c no matter how hot it is, so there ya go.
PS: how goes the auto to manual junk, I dropped you a line but it says you haven't gotten it yet.