This is an article that names 5 things to help you save money in Japan. I would add a couple of more tips to it though. This is their 5 things:
1. Don't take the taxis-They are like private limos
2. Get a Japanese rail pass-Train tickets are super expensive and the JR pass will save you a ton.
3. Eat at convenience stores-enough said, they have more than just chips and candy
4. Walk everywhere-duh
5. See the free things-There are some government buildings that have observation decks and are free.
This is what I would add:
1. Get a metro pass-It will save you money and time not spent of fumbling at a ticket kiosk. In Tokyo you can get it along with an airport shuttle ticket (website) and it's a really good deal. There is also another pass in conjunction with the airport express train (website). These passes and JR passes are only available to foreigners and the JR pass must be purchased outside of Japan. The others can be purchased in Japan but you need to show your passport.
2. Vending machines-In Japan, everything is in a vending machine. Some (if not most) aren't in English though. But they are cheap ways to get a cold drink or snack.