I am no expert on punctuation, nor do I care much for its correct or incorrect usage much (and neither do most people, as far as I can tell), unless the punctuation changes the meaning of the sentence, which is very rare. However, I'll try my best to answer:
1)It's often sung, but I have a preference for the violin versions.
2)It's often sung but I have a preference for the violin versions.
Here 1) is correct. The rule with "but", "end" and "because" is that if the sentence portion after those words is a complete sentence, then you should use ",", otherwise - no ",".
E.g. "I like violin music but not piano.", but "I like violin music, but I don't like piano music".
And I think Mun Hwan is correct about comma after "so".