The Riff-Raff Cinema and the Arthouse Group have a shared reservation system, so you only need to register once. Online reservations can be made over:
http://www.riffraff.ch/
http://www.arthouse.ch/

The repertoire cinemas Xenix and Filmpodium also offer online reservation for tickets, but not for individual seats.
http://www.xenix.ch/
http://www.filmpodium.ch/