You have set up joints for what will be your character rig in Maya, and wouldn’t you know it, some don’t rotate correctly. Likely, it is due to the joint’s rotational axis being off from the rest of the joints in the rig, chain, or itself.
…you’re about 90% done orienting your joints. The trouble is, when you start to rotate your chain, you realize the current primary axis is not the one you wanted.
You can alter these rotational axes simple enough, but how to you know you are getting even close to being accurate? You could use Character and Rigging TD, Bryan Godoy’s ezJnt script for Maya. The script lets you use geometry topology to create joints that are oriented correctly, really quickly.
That doesn’t mean that you can do it manually, though. As shown here by Bryan, you can easily flip the primary axis for joints by simply using a rotational snap.
Of course Bryan uses his ezJnt script along the way, but that is simply out of convenience. The script is free, however, so why not download it and give it a try.