The article Mapping Music in Harvard Magazine (January-February 2007) describes a technique that uses non-Euclidean geometry and ideas from string theory to map chords. Very cool. This may provide some insight into the question of why certain note combinations are percieved as dissonant or consonant, and why some chord progressions "work" while others do not.
The guy behind this, Dmitri Tymocko, has a website here that includes the paper he published in Science on this (the first musicoloy paper in Science's history) along with movies and software to plot chords yourself. I am definitely using this the next time I teach acoustics!