[gtani]

    Why do some note combinations sound good.  

This is a discussion of equal temperament vs. just intonation ratios

http://irkenkitties.com/blog/2012/11/28/consonant-intervals-...

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You can read a lot in the subreddit

http://www.reddit.com/r/musictheory/comments/16h5fk/how_do_y...

http://www.reddit.com/r/musictheory/comments/16gl5h/a_questi...

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Equal temperament instruments present all kinds of problems, wolf intervals in the extreme (Pianos have inharmonicity/octave stretching, flutes effectively have octave stretching, guitars have all kinds of funkiness

http://www.truetemperament.com/

https://en.wikipedia.org/wiki/Wolf_interval