I bracket frequencies of instruments prior to a mix, and use a real time FFT display to assist. Yes they show as peaks,... but so do the partials. Some fancy filtering might help to bring out the notes and less of the partials.
I use a DAW with an EQ (which I leave bypassed to just use the FFT) that has a real time FFT display capability. Found the FFT to be useful.
Also check with C4DM at QMUL and CCRMA at Stanford, CA, USA. There are some people doing some interesting work along those lines.