I would say there's just too many things that affect it, the things I've heard that increase sustain is hilarious!
I would imagine the body and neck joint being very important, due to the strings being anchored to "the guitar"
Then i would say that the bridge would make a huge difference, you always hear about how guys upgrade their strat saddles and trem blocks to stell as it resonates better than that die cast crap and zinc blocks.
3rd i would say that the strings themselves would account for it too.
Rotosound's for the win!