When building a skeleton, consider which skinning method you eventually want to use. Building a skeleton for an object that is to be smooth skinned requires a different construction strategy than building a skeleton for rigid skinning or an indirect skinning method such as lattice or wrap skinning.
For example, since smooth skinning enables gradual deformations that can be influenced by several joints, you can use joints to create deformation effects that resemble breathing or muscle action. Using joints for this would not work very well with rigid skinning. Instead, with rigid skinning you would use flexors to create similar deformation effects.