Eric Lippert has a very interesting series of articles dealing with temperment and other related math/music matters:

Desafinado, Part One: Eric Continues His Obsession With The Greeks
Desafinado, Part Two: A Perfect Pythagorean Tuning
Desafinado, Part Three: Too Many Fifths
Desafinado, Part Four: Rolling Your Own WAV Files
Desafinado, Part Five: Getting Down Without Hitting The Bottom