The metro system
The Tokyo metro system is one of the most complicated in the world. There are at least three different parallell system and private railways with separate stations and competing lines, often with similar names and locations. To calculate the fare by and buy the correct ticket is complicated too, as station names are only given as Kanji on the big board over the ticket machines. However things are easy too. Just get a Pasmo/Suica card for automatic payment, and use google maps to tell you which line to use. Easy and painless. Cards cannot be topped up with a credit card only cash.