Tuning: Just Intonation
When one uses harmonics to tune (a process too lengthy for me to describe here), a tuning methodology that favors the fractional lengths of the string to determine pitch of other notes is called Just Intonation. Many people describe this method as 'what your ear wants to hear'. Others disagree. I'm an agnostic, myself. I prefer something in between
the tonic chord (E for E9; C for C6) sounds in more in tune to many people's ears than an evenly spaced EQUAL TEMPERAMENT tuning.
the third is flatted about 14 cents and the b9 (like F on E9) is 28 cents (nearly 1/3 of a fret) flat -- compared to ET
There is more information on Just Intonation on this page