IANAM (I am not a mathematician), but a FFT is basically modeling a complicated periodic function by the addition of overlapping sine and cosine functions. The equation of a Fourier series is: (ah, for LaTeX format; sigh)
f(x) = 1/2 a0 + the summation from n=0 to infinity of an cos(nx) + the summation from n=0 to infinity of sin(nx).
The Fourier transform is: f(x) = integral from negative to positive infinity of F(k) * e^-2pi*i*k*x dk. What all those variables are, I have no idea. Lots of math manipulation Setiathome uses FFTs to try to find patterns in the periodic waves and fit curves to the distributions of values. I've been reading about them in analyzing the dark noise in rod cells; a current is continuously produced in the abscence of light stimulus, which has various types of noise produced from transduction mechanisms and random release of synaptic vesicles.
hth.

Chocolate Pi (still in MacOS without my cookie but with Appletalk that recognizes the printer)