Guest, I doubt that the frequency that we use to base other notes on like A=440 has much to do with much of this. I think it has more do do with the ways we have divided the frequencies to make our scales and I found well temered scale article that Pene pointed to interesting.

With regards to the original question, I don't know why say the guitar is tuned to the notes it is but having chosen that, the fact there are more open strings available in E is likely to make something sound different to say F. We can get onto a whole new (probably discussed many times) subjects like the merits of DADGAD... if I keep those thoughts up.

Jon