This is a part of the Before You Ask segment
PUBLIC TRANSIT IN JAPAN
If you are doing more traveling than basing yourself in 1 city and doing daytrips, Google Map is your friend when planning routes from station to station. However, Google Map is not always accurate on schedules, lacks bus routes in Japan, and there’s limited options. This is where Hyperdia comes in. It’s completely text-based, so you better know the exact romanized spelling of the station, but it has the added bonus of being able to choose if you’re traveling by JR Railpass or not.
on checking Trains Routes
on all kinds of Rail Passes
on Buses
on Taxi Fare calculations
Taxis are common in Japan, but they’re also quite expensive and should be used only if there are no other alternatives, like visiting the tuna auctions at Tsukiji Market at 4am.
ON LUGGAGE STORAGE AND TRANSPORT OPTIONS
Luggage storage and transport options for easy traveling across the country.
- Ta-Q-Bin for Airport - luggage transport service between airport and hotel/home.
- Ta-Q-Bin Handsfree Travel - send your luggage to the next hotel at the reception desk of the current hotel.
- Ecbo Cloak - a new service to take advantage of unused spaces in shops, cafes, and even post offices.
- JAL ABC - airport luggage delivery service from Japan Airline.
- Sagawa Express - similar to Ta-Q-Bin, luggage storage or transport service across the country.
- Rail Go Service - multi-day luggage storage service, in a niche corner outside Tokyo station.
ON CAR RENTAL
Tocoo is the rental service middleman of choice, and the price point to compare with other booking agencies.
Niconico Rent A Car is an alternative cheaper choice. They rent older model 2nd hand cars, generally at a cheaper rate than most of the competition, but their branches are very limited.
Tabirai is a newer one to add an English interface, they are a middleman company similar to Tocoo, but perhaps with a nicer looking website, with fewer options.
and also JR Rent A Car (or Ekiren), this is the rental car company at many train stations, with discounts if you have certain rail passes.
Toyota is the most common rental company for foreigners.
Nissan is also popular with a good English website.
Other companies includes (but not limited to): Times, Nippon, Orix, ...
Info on ETC (Electronic Toll Collection)
Info on various Expressway Passes
On ETCs, as a traveler who drives often in Japan, and while I'll still use it on occasion, I really can't recommend using the expensive tolled expressway system. The point of driving as a tourist in Japan is to have more flexibility than taking public transit, so why get on the expressway that only has limited points to escape from? Plan your itinerary accordingly and drive on national highways and regular roads. There are tall noise barriers that block most of the views on many parts of tolled expressways. On the other hand, if you must travel on them, one bonus is you can get a sample of some local specialties by stopping at the many grandiose service areas (Service Areas, not Parking Areas which are just glorified toilets).
Also, while Hertz and Avis are available in Japan, of all the years in many Japan travel groups in multiple languages, i've never heard either of the names mentioned even once. Hertz I've recently learned has no physical presence in Japan but instead they are partnered with Toyota Rent-a-car, so you can still get member points if you rent through Hertz's website. Avis is only limited to Shin-Chitose airport in Hokkaido and Fukuoka airport in Fukuoka.
Please do be careful driving in Japan. It's easy to be distracted by the sights and get lulled into a false sense of safety, but tourist accidents by rental car is quite commonplace. Learn what to do if you do get into an accident. Better yet, learn Japan's house rules on the road (and here and here).