Daniel C.
Yelp
For our 1-week vacation in Tokyo, we chose our hotel to be close to a train station for convenience. The Shinjuku Station is the mother of all subway stations, likely the busiest one in the world. Its very complicated with virtually every train line running through here. The advantage of course, is that you have multiple ways of getting to/from here if you make this your home base.
It took us days to get used to navigating the station. Initially we were dazed and confused upon entering the station the first time. They have JR lines (labeled JR) and Tokyo Metro lines (each one colored and given a capital letter) than run all over the city. You can (and sometimes will) transfer from Metro to Metro, and Metro to JR or vice versa. Use Google Maps to plan your route outside the station, its a lifesaver! Inside the station, follow the many signs that point to your train. Double check you're on the right platform after that!
There are also multiple commuter cards that charge you different fares based on JR, Tokyo Metro, and whether you plan to travel out of Tokyo using a bullet train. If staying in the limits, we used the Suica card which costs $5 US deposit and can be loaded/reloaded easily at many machines.
To make things even more complicated, there are multiple exits and multiple levels. There are paths leading to entire malls and even a university! Follow the signs! After a week, I still haven't figured out how to walk from the West Exit (where my hotel is) to the East Exit (where all the good eats and shopping are) from inside the station!
If there's one consolation to all this madness, its that there are lots of good restaurants inside the terminal, including a good Onigiri place for breakfast near Area B in the West Entrance. We also had good soba near the path leading to the Oedo line from the West Entrance. Plenty of restrooms too that are reasonably clean.
Also, despite the massive amounts of people (perpetual rush hour), somehow the system is very efficient at moving people through. Trains come often and unlike BART back home, almost always run on time and are much cleaner and air-conditioned!