I'm chiming in here mainly to see if there is a simple answer. Like Cage, I rarely venture in to the setup room, and it usually seems easier to re-rig something if a mistake has been made.

Quote - My impulse is to suggest that for most body parts the rotation order probably does matter, but I haven't done extensive tests to verify that.

I've seen it suggested when building hierarchy files that the first axis should be along the direction of twist, and if possible the second axis in the rotation order should be the most-used bend. So for a forearm on a T-posed figure, the order should be XYZ: it would twist around the X axis, then bend mainly in Y. Z equates to side-side, which a human figure's forearm doeswn't usually do.