I'm working with the FFT, and I've found that it output certain frequencies, but not all. If I input a 440Hz sine wave with 4096 samples, there is no 440Hz response, but instead it's distributed among a few frequencies, like:
... 421.875Hz: (mag: 0.207764, phase: 0.140608), 433.594Hz: (mag: 0.580138, phase: 0.144488), 445.313Hz: (mag: 0.690567, phase: -2.99323), 457.031Hz: (mag: 0.212671, phase: -2.98935), ... Since the FFT is a lossless transformation, it appears that you can represent a sine wave as the sum of multiple sine waves of different frequencies and phases. I don't know the formula for this transformation, however, and I'm not sure how it works (I haven't experienced playing multiple different notes and having them end up as a totally different note, but that doesn't mean it's impossible).