Traditionally, Japanese was written top to bottom, right to left. You can still see this in newspapers and some magazines, as well as on plaques, certificates, or other official documents.
Recently, though, for reasons I am not positive of (can anybody fill this in), Japanese is often written left to right, top to bottom now. This is apparent in many books and magazines, menus, and other documents. Some of these are still written in the old style, though. It is up to the author. I have a bunch of Japanese books and some are written in the old style while some are in the new. I work at a Japanese middle school, and looking at how teachers write on the blackboard reveals that both styles are used here as well.
So there's not really an easy answer. Seems to be fair game for one of two styles.