Bargaining (haggling) with a seller to lower the displayed price of goods is typically not a custom in Japan.
If it says "1,000 yen" then it means 1000 yen and usually wont be discounted.
You can however get "discounts" in the form of point cards. The most generous point cards are for electrical stores like Bic Camera and Sakuraya. Sometimes they give up to 20% worth of the purchase price back on to your card - great for when you are buying expensive stuff. Simply put, if you spend 10,000 yen on something then you get to spend 2,000 yen on whatever you want on your next purchase.
Anybody can make these cards even if you are a visitor to Japan. If you are buying electronic goods, bring along your passport too and you don't have to pay the consumption tax which is currently 5%. Point cards and passport = a *lot* of savings to be made which you can then spend on figures and stuff.
Just out of interest, how much is the consumption tax in your region? I remember it being something like 17% when I lived in the UK.