1) If they're similar to a Terran species, just keep the same basic features. So a catlike alien would tend to have vertical slits. This is helpful if you want to use some of the really weird shapes.
2) If they're not similar to a single species, look for parallel evolution. Were their ancestors predators (vertical slits), prey (horizontal slits) or active foragers (round)?
3) If they have a totally different shape, make sure you provide an explanation that makes sense. Frex, hourglass pupils might have a separate rod/cone mix, so that each half would dominate under different lighting conditions.