I don't have any good web links, but a couple of books that I've found useful are The Science of Musical Sound by John R. Pierce and Harmonic Experience by W. Mathieu. (The former is more focused on sound and scientific theory, whereas the latter is more focused on understanding music in a way that would be useful to a musician or composer.)
On the Sensation of Tone by Helmholtz is also worth checking out if you want to understand where a lot of the modern understanding of just intonation comes from.
On the Sensation of Tone by Helmholtz is also worth checking out if you want to understand where a lot of the modern understanding of just intonation comes from.