This is a direct quote from seventy6ty on cgtalk.com, where he explains a little about joint orientations. I put it here for reference.
Well, different people have different preferences. The method I've adopted, after seeing the pipeline at R+H and Sony, is to have X pointed down the joint's axis, to be used for the twisting attribute. There is a general method that is even used in physical injury specialists, of having X being the twisting attribute of any joint. Then, using the Z-axis as the most commonly bending axis. So, on a knee, the Z-axis would be the one you use to bend it. On the shoulder, the Z-axis would be used to elevate the arm, etc. Then Y is used as the secondary rotation axis.
So on an abdomin, X would twist, Z would be front to back, and Y would be side to side twisting.
I still have yet to fully understand the xyz rotational axes evaluation. I usually just play with them a bit for each joint until I get it evaluating correctly, with the IK for that joint chain. The way I understand it, it actually goes backward, the z, in this case, being evaluated first, then the y which is it's parent, then the x which is the top parent of all these rotations.
Hope that helps a bit.
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