For the majority of optical systems it is typically assumed that the transmitted wavefront has uniform (or Gaussian) amplitude and constant polarization state. This is the default assumption of geometrical optics. This paper considers methods suitable for analyzing systems where this assumption is not valid. Such methods of polarization analysis include polarization ray tracing and polarization aberration theory. Definitions of the basic classes of polarization phenomena and a review of the Jones calculus are included to form a basis for the discussion.