I am developing software that depends on musical chords detection. I know some algorithms for pitch detection, with techniques based on cepstral analysis or autocorrelation
See my answer to this question: How can I do real-time pitch detection in .Net?
The reference to this IEEE paper is mainly what you're looking for: http://ieeexplore.ieee.org/Xplore/login.jsp?reload=true&url=/iel5/89/18967/00876309.pdf?arnumber=876309
The harmonics are throwing you off. Plus, humans can find fundamentals in sound even when the fundamental isn't present! Think of reading, but by covering half of the letters. The brain fills in the gaps.
The context of other sounds in the mix, and what came before, is very important to how we perceive notes.