Here are a few tips for cheap and convenient traveling in Japan:
This is for school holidays only. Gives you 10 days of traveling for one month. You can use the days whenever you want, so its perfect for making bigger trips in Japan. You can only use it on specific trains though, so the trips will be longer but a lot cheaper then paying the full price.
This is the essential travelling card. It works very simply, you put money on it and going in and out of metro or train you beep it on the gates and you get charged the exact amount for the distance you made. Can be also used to buy stuff in some shops and even at some drink machines. Very handy, makes your travel a lot easier.
This is for a one day free travel in Tokyo. There are multiple versions, just metro, metro and train, etc. I used the metro one. 600 yen for all day metro traveling is a nice deal and kind of a necessity if your place is a bit more out of the center.