Hi all, thanks for your comments and questions - yes I've been working on the algorithm for years (you'll see a couple of academic papers over at http://www.idrumtune.com
It is doing much more than a simple guitar tuner, you are right. The iDrumTune software looks at all the frequencies generated and uses a unique algorithm to select the fundamental to display. But actually the software also displays the full frequency spectrum in graphical form, so you can look closer and see what the overtones are at the same time. This way it's really simple to know which frequency you are looking at and measuring. Obviously the lowest frequency is the fundamental and the second is the first overtone which can, as you said yourself, be used to help tune around the perimeter of the drum.
Actually the benefit of using an iPhone is that you can move the microphone above the position of the lug you are tuning, so you get a very accurate reading of how the drum is vibrating at that exact lug. In my experience it is not possible to accurately tune each lug without moving the microphone to the point of excitation.
I hope that helps answer a few questions, feel free to keep them coming :) and thanks for your interest!