Hydrogen vacancies in graphane are products of incomplete hydrogenation of graphene. The missing H atoms can alter the electronic structure of graphane and therefore tune the electronic, magnetic, and optical properties of the composite. We systematically studied a variety of well-separated clusters of hydrogen vacancies in graphane, including the geometrical shapes of triangles, parallelograms, hexagons, and rectangles, by first-principles density functional calculation. The results indicate that energy levels caused by the missing H are generated in the broad band gap of pure graphane. All triangular clusters of H vacancies are magnetic, the larger the triangle the higher the magnetic moment. The defect levels introduced by the missing H in triangular and parallelogram clusters are spin-polarized and can find application in optical transition. Parallelograms and open-ended rectangles are antiferromagnetic and can be used for nanoscale registration of digital information.