I have implemented Demetri\'s Pitch Detector project for the iPhone and hitting up against two problems. 1) any sort of background noise sends the frequency reading bananas
The frequency response function of the iPhone drops off below 100 - 200 Hz (see http://blog.faberacoustical.com/2009/ios/iphone/iphone-microphone-frequency-response-comparison/ for an example).
If you are trying to detect the fundamental mode of a low guitar string, the microphone might be acting as a filter and suppressing the frequency you are interested in. There are a couple of options if you interested in using the fft data you can get - you can window the data in the frequency domain around the note you are trying to detect so that all you can see is the first mode even if it is of lower magnitude than higher modes(i.e. have a toggle to tune the first string and put it in this mode).
Or you can low pass filter the sound data - you can do this either in the time domain or even easier since you already have frequency domain data, in the frequency domain. A very simple time domain low pass filter is to do a time-moving average filter. A very simple frequency domain low pass filter is to multiply your fft magnitudes by a vector with 1's in the low frequency range and a linear (or even a step) ramp down in the higher frequencies.