Barbie: «Don’t you just love the subway? I just have to set foot on a subway train, and it’s like a magic carpet. Y’know? It could take you anywhere.»
Wanda: «Yeah, that’s what I’m afraid of.»
Sandman «A Game of You» by Neil Gaiman
One recommendation for Tokyo was to use IC cards which you can recharge and use to pay for the trips. You can buy them at the airport (vending machines) and charge them with a few thousand Yen. If you need to add money later, you easily do so in any subway station.
With such a card, you simply swipe it when entering a subway station, take the subway to your destination, and swipe them again. The amount is taken from the card.
And yeah, that is nothing special, that exists in lots of cities.
But these cards also work in other cities, at least in Kyoto. They can also be used at vending machines for drinks, which you need to use multiple times during the day due to the hot and humid weather. You can also use them to pay in some stores, e.g., at Starbucks. And finally, the subway trips are really cheap.
Overall, a great system.