Google Maps
Best overall navigation with train/bus schedules in Japan
Japan Travel Tools: JR Pass, Budget, Weather & Sight/Shop | HaniSeoul
Practical Japan travel tools for airport transfers, JR Pass planning, budget, prices, packing, tax-free shopping, and destination planning.
Navigation
Japan Transit (乗換案内)
Detailed train transfer routes and fare info
Taxi
GO Taxi
Most popular taxi app; accepts international cards
Translation
Google Translate
Camera translation for menus and signs
Payment
Suica / Apple Wallet
Tap-to-ride transit card for trains, buses, and convenience stores