Berlin has an amazing amount of cinemas. You don't have to be scared to have to see a film twice, even if you go to the movies every single night. There's only one (minor) problem: if you don't speak German, the selection is less wide, because most Germans (not all!) like their movies synchronized (I could never and still can't understand why - even after many hours of discussion with some friends). For the entire program, check zitty or tip. If the program indicates the letters OmU, it means "Original mit Untertitel) that the film is in original language with German subtitles. Note also, that on Monday (for some cinemas also Tuesday) is "Kinotag" where you pay less. Here I will mention my favorite cinemas either because of the architecture or the program.
Arsenal
If you are a real cinemaniac, you will love this one. This is a movie theater with excellent film cycles. One of them is called the Magical History Tour where they show every day an important movie of film history. If you went there for one year everyday, you can definitely call yourself a film expert... and maybe also a cinemaniac. Potsdamer Strasse 2.
Babylon Kreuzberg
Here, the films are always in OmU. They have a good program with current movies. Nice cinema. Dresdener Strasse 126.
Babylon Mitte
Another good cinema that shows old movies. They have a good program and it's a nice old movie theater. Sometimes they also have live music supporting silent movies. Rosa-Luxemburg-Strasse 30.
fsk am Oranienplatz
This cinema mostly shows Asian or other world movies. I have seen some good Japanese movies here. Unfortunately, the subtitles are often only in German. Segitzdamm 2.
Kino International
This is my favorite. They mostly have one film playing during a few weeks, but the architecture is just too cool to be true. It is the former movie theater for the opening of films in the GDR. Go early enough, so you can have a drink in the lobby on the first floor and the view onto the Karl-Marx-Allee 33.
Tilsiter Lichtspiele
This is a little neighborhood cinema in the back of a cafe/bar. If you have missed a film that is not too old, you might have a chance to see it there. They have a good selection of films and it is a cute place. Richard-Sorge-Strasse 25a.