Many stores still do not take credit cards.
A lot of convenience stores will take credit cards, most will take Suica cards (mass transit cards pre-loaded with money). Some vending machines will take Suica cards.
Mobile phone payment is kind of a hassle and requires a credit card as well as a phone that supports it (osaifu keitai). Not all phones do.
Cash is still the preferred method of payment online too -- three of the four options are basically cash: bank transfer (done with cash at an ATM or online if you use a bank that supports it), COD, and payment at a convenience store.
