'Cuz that's how we roll these days...
Hyperdia, gives you all the Japan Rail Pass schedules and is super easy to use. Type in your location and destination, and it provides several options with times, trip duration, platform numbers and any extra fees.
Tokyo Metro app is simply amazing. The subway is also simply amazing. Clean, on time, easy to figure out, screens in every car showing not only what the next stop is, but what car you are in and exactly where it will stop in relation to stairs, escalators, and exits. Signs at each stop make it easy to figure out which exit out of the subway you want - none of this "SW corner of 42nd St and Broadway" nonsense (yes, hello NYC). Type in location (or enable location services and it will do it for you), destination, and it maps it all for you including stops, transfers, cost, trip duration.
Google Translate deserves its own post, but suffice to say Waymo, the other translation app recommended by several travel sites, is not even close. They both access your camera for real-time translation although that's problematic in both apps. Both allow you to "submit" the camera image for more accurate results if you have wi-fi or cellular data service. Google for the win here.
Still being tested - Travel Japan Wi-Fi and Japan Connected, both apps that find free wi-fi on the go. So far, it kinda works.