orienting joints of a skeleton after positioning them in a character’s mesh is extremely important. without double checking them you’ll experience a lot of troubles as soon as you are playing around with your rig. theoretically if you don’t edit a skeleton at all, you don’t have to orient the joints since the rotation is set automatically when creating them, but this practically never happens: you’ll always edit your skeleton somehow, so fixing or checking the local orientations of all joints is a must. die-hards can still orient all the joints manually by selecting all joints, displaying the local rotation axis (display > transform display > local rotation axis), accessing component mode (f8), switching the miscellaneous selection mask in the status bar to local rotation axes (right-click on the ‘?’ icon) and then rotate each joint step by step. nowadays maya offers a little helper: skeleton > orient joints.
i prefer to have the y axis going down the bones – just because you’re used to this in maya when you are for example rotating an object around the y axis and you know exactly what this means. how you want to orient the z and x axis is just up to you – you just should stay consistent and this command will help you to do this. after orienting you can see that the last joint (e.g. at a finger tip) is still not orienting correctly, but that doesn’t matter since a end joint doesn’t have to control an attached bone.
another interesting way is to create a completely new skeleton by just point snapping (v) new joints to the old skeleton (which you’re happy with but didn’t orient the joints yet). this way you create a fresh new skeleton you’re not going to edit so the rotation of all joints are (automatically) perfectly fine. don’t forget you shouldn’t click on the first joint of the old skeleton else you’ll attach the new joints to it. instead, just click a little next to the start joint and because you have point snap on, it will still snap to the joint, but not attach the new bone structure.
p.s.: for those who are confused by the standard tool maya offers, rigging god jason schleifer wrote a little script many years ago which is still just a tad clearer than the standard tool. his mel script is called jsOrientJoint (nomen est omen) and fulfills the task really straightforward. grab it here as i couldn’t find it on any download site any more.