Besides the normal mainstream cinemas, there are three noteworthy cinemas in this city. That might not be much, but the program they offer is amazing.
My absolute favorite cinema for older films and retrospectives is the CAC Voltaire at 16, rue General Dufour at the "Maison des arts du Grütli". I can not say how many hours i spent in this cinema during my university years.
Les scala is a very good cinema for current independent movies from all over the world. You only need to look at its program to know how international Geneva is as a city.
If you feel more experimental go to the Spoutnik at the usine. This is a very cute small cinema with an interesting program.