Just a comment: The fundamental harmonic may as well be missing from a (harmonic) sound, this doesn't change the perceived pitch. As a limit case, if you take a square wave (say, a C# note) and completely suppress the first harmonic, the perceived note is still C#, in the same octave. In a way, our brain is able to compensate the absence of some harmonics, even the first, when it guesses a note.
Hence, to detect a pitch with frequency-domain techniques you should take into account all the harmonics (local maxima in the magnitude of the Fourier transform), and extract some sort of "greatest common divisor" of their frequencies. Pitch detection is not a trivial problem at all...
DAFX has about 30 pages dedicated to pitch detection, with examples and Matlab code.
