Musicians like Jon Catler have incorporated microtonal guitars like 31-tone equal tempered guitar and a 62-tone just intonation guitar in blues and jazz-rock music.

Check out Jon Catler playing in Just Intonation at: http://youtu.be/8AYlsLNTjrc
Jon Catler playing the 12-Tone Ultra Plus guitar: http://youtu.be/O2eukIoSsKM
More Jon Catler: http://youtu.be/MU27AhOuwSE

The "Just Scale" (sometimes referred to as "harmonic tuning" or "Helmholtz's scale") occurs naturally as a result of the overtone series for simple systems such as vibrating strings or air columns. All the notes in the scale are related by rational numbers. Unfortunately, with just intonation, the tuning depends on the scale you are using - the tuning for C Major is not the same as for D Major, for example. Just intonation is often used by ensembles (such as for choral or orchestra works) as the players match pitch with each other "by ear."

The "equal tempered scale" was developed for keyboard instruments, such as the piano, so that they could be played equally well (or badly) in any key. It is a “compromise” tuning scheme. The equal tempered system uses a constant frequency multiple between the notes of the chromatic scale. Hence, playing in any key sounds equally good (or bad, depending on your point of view).