K Tyler, this is for you!
According to my basic knowledge of rigging, joint orientations on the hand all depend on the direction the digit will be rotating. Fingers are most often rotating "up" or "down". The thumb is a lot more interesting orientation wise, because it will be rotating "in" and "out", and most likely on a slight angle.
This example is the joint orientation of the bind chain in the free Zombie Rig from Sony. They have the -Y pointing down the chain, as opposed to our +X.
Hope that clears things up.
This is Tyler. Yes, that does clear things up a lot. I have all the joints in the hand but they kind of look like a bowling ball smashed them a little. It's just not as nice and straight as it should be. I'll fix that.
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