The way modern instruments are tuned, in what is referred to as "Equal Temperament", is, relative to musical history, a recent phenomenon. Rather than having every half step the same ratio, such that every scale of the same type (e.g., major or minor) sound exactly the same, most older music is tuned so that each note has the best interaction of frequencies with a tonal center. Some folk instruments that use drone techniques, such as bagpipes and mountain dulcimers, still use these older tunings.
I plan to post some specific files here for those curious about the tunings I use (some of which I personally invented) in my recent recordings. Until then, I am posting some links here to some sites and tools for those who would like to learn more, and experiment with alternate tunings in their own music.