JR do different passes for different areas too.
There are also various day passes for JR trains,private subways, private trainlines, busses or any imaginable combination of the above.
check out
JAPAN RAIL PASS / ジャパンレールパス
and the various JR group links for the areas you will be in.
The more research you do the more you will save.
Transportation in Japan
is a good place to start.