Japan's larger cities are serviced by subways or trams, buses and taxis; indeed, many locals rely entirely on public transport.
All cities have public bus systems but it is unlikely that you will find yourself riding them often; Kyoto is the big exception. Smaller cities that don't have subway or tram services usually have a tourist bus that does a loop to the main sights starting and ending at the main train station. City buses typically have a flat fare; day passes are often the most economical way to get around.
Buses that head out of cities or traverse rural areas calculate fares based on distance. When you board (from the rear door most likely), pick up a paper ticket marked with a zone number from the dispenser; when you get off, match your zone number to the electric signboard in the front of the bus and put the posted fare and ticket into the fare box, or show the driver your ticket and a handful of coins and have him or her pick out the required fare; they're used to this.
All buses have change machines near the front door that can exchange ¥100 and ¥500 coins and ¥1000 notes.
Ride-sharing apps are regulated in Japan. A commercial licence is required to qualify as a driver, so an app like Uber will connect you with a private town car (and probably cost more than a taxi).
Subway systems operate in Fukuoka, Kōbe, Kyoto, Nagoya, Osaka, Sapporo, Sendai, Tokyo and Yokohama. They are usually the fastest and most convenient way to get around the city. The Tokyo metro area and Kansai metro area are further linked by a network of JR and private rail lines. Stops and line names are posted in English. Rides cost from ¥160 to ¥200.
If you plan to zip around a city in a day, an unlimited-travel day ticket (called ichi-nichi-jōsha-ken) is a good deal; most cities offer them and they can be purchased at station windows. If you plan to spend more than a day or two, then getting a prepaid IC card is highly recommended.
Smaller cities have tram lines. These include Nagasaki, Kumamoto and Kagoshima on Kyūshū; Hiroshima on Honshū; Kōchi and Matsuyama on Shikoku; and Hakodate on Hokkaidō. These usually offer unlimited-travel day tickets.
IC cards are prepaid travel cards with chips that work on subways, trams and buses in the Tokyo, Kansai, Sapporo, Niigata, Nagoya, Okayama, Hiroshima and Fukuoka metro areas. Each region has its own card, but they can be used interchangeably in any region where IC cards are used; however, they cannot be used for intercity travel.
The two most frequently used IC cards are Suica from JR East and Icoca from JR West; purchase them at JR travel counters at Narita and Haneda or Kansai airports, respectively. Cards can also be purchased and topped up from ticket vending machines in any of the cities that support them. A ¥500 deposit is required to purchase a card; you can get the deposit back by returning the card to a JR ticket window.
To use the card, simply swipe it over the reader at the ticket gates or near the doors on trams and buses. They can also be used to pay at some convenience stores and vending machines.
In Japan, finding a place from its address can be difficult, even for locals. Addresses are not designated by streets, but rather by concentric areas and blocks and then a building number, which may or may not be consecutive with the ones around it. Smartphones with navigation apps have been a real boon for travellers – probably the biggest reason to want a stable, consistent wi-fi connection at all times. In cities, ubiquitous kōban (police boxes) have maps, and officers are always happy to help with directions (though few speak English).
Baggage courier services (called takkyūbin) are popular in Japan and many domestic tourists use them to forward their bags, golf clubs, surfboards etc ahead to their destination, to avoid having to bring them on public transport. The tourism bureau has been working to open this service up to foreign travellers; see its guide, Hands-Free Travel Japan (www.jnto.go.jp/hands-free-travel), for a list of luggage forwarding counters, mostly at airports, train stations and shopping centres, set up for travellers.
This is a great service except for one caveat: in most cases, your bags won't get there until the following day. (So, for example, if you want to ship your luggage to or from the airport, you'll need a day pack with one night's worth of supplies.) On the other hand, this can free you from large luggage for a one-night detour to an onsen – just send your bags to the following night's destination.
Hotels can also often arrange this service for you (and the couriers will pick up the luggage from the lobby). Costs vary depending on the size and weight of the bag and where it's going, but it's typically around ¥2000.