There are actually two overlapping train systems, the metro and JR rail. The well-thought-out organization is a pleasure to behold. Here's three of my favourites.
- Maps. At every station, there are large, clear maps of the system, in English and Japanese, showing the routes -- but the best part is that beside each station's dot on the map the time it takes to get there and the cost of the trip.
- Movement management. With lots of people and huge stations, management of people is key. Arrows are painted directly on the floor and the stairs showing where you should be walking if you're going that direction, so people aren't crashing into each other like Mongols riding into battle. And people (mostly) comply!
- Music. On the JR line, each station has its own little tune that is played before a train departs. Daydreaming commuters, or those who can't understand the announcements (which are in Japanese and English) just have to recognize their tune (before the doors close).