Getting around in Tokyo

So you somehow made it to your hotel and you are ready to go see the sights. Now what?

[Update, Nov. 2019]

They either did not have them back in 2012, or else I missed it. But you can buy fare cards that will work on at least JR, some subway lines (haven't tried Toei), and buses. Get one at a machine in a subway or train station. There is English and they take credit cards. Then simply tap it on the reader whenever you encounter a gate or a fare box. This greatly simplifies some of what I describe below.

Also, once you know the system a little better (or simply get caught unprepared), the trick is to make your way to a major train station (e.g. Shinjuku) and find a large ticket office. Generally, someone there will know just enough English to be able to help.

[end update]

The best way to get around in Tokyo is the subway/train system. If you are not used to taking the subway, this can be a new and intimidating experience. If you are already used to taking the subway, it still takes some time to get used to the subway system in Tokyo, for 2 main reasons:
1) The vast majority of the time, fare maps have no English on them
2) You have to juggle multiple subway systems to get from point A to point B.

Tokyo is a little unique in this respect. They have the JR system, the Tokyo Metro system, and the Toei system (plus some privately owned train lines that are only of importance to go outside of Tokyo). The systems do not talk to one another. You can't transfer directly from a Metro line to a Toei line. You have to exit and get a new ticket and many times, walk to another station.

Here are some tips on using the subway system in Tokyo
1) Learn to recognize the logos for each company.

Toei

Metro

JR

2) Invest in a bilingual map. You can get by with an English map and comparing it with the Japanese map posted in the station, but with a bilingual map, you can easily match up the English with the Japanese. It's convenient, safer, and educational.
3) Don't let these subway entrances intimidate you. It can feel like you are walking down into hell without knowing what's at the bottom. Just go down and have a look-see.
4) Look for ticket vending machines and system maps. Get out of the way of busy locals, take a deep breath and collect your thoughts. As long as you stay out of their way, people will let you be lost and confused for as long as you need to be lost and confused so there is no rush.
5) Pull out your bilingual map and figure out how to get to where you need to go, preferably using the same system as the one you are standing in front of.

6) Compare your map to the fare map on the wall. You are looking for your final destination, at least with that company. From here it's relatively simple. The station you are in is highlighted on the map, usually by a gold box with some mysterious characters in it, as opposed to numbers. Look for your destination and note the number in that box. That is the fare you have to pay.
7) Prepare bills and coins and approach one of the ticket machines. If they have a button that says "English", go ahead and press that. It's pretty easy after that. If there is no "English" button, it's still pretty easy. Press the button that has your fare amount on it. Put in the money, out comes a ticket and your change.
8) Make careful note of two things: A) The name of the line you are taking. B) The station at the end of the line, or at least some big station along the way.
9) Go through the gates by inserting your ticket into the slot (watch people for a while to figure out how that works before you go in). Your ticket comes out at the other side. Make sure you pick it up and carefully hold on to it, you will need it to exit at the end. THIS IS VERY IMPORTANT.
10) Follow the signs to the train you need (match the line name and the end of the line station). Once on board, keep track of the stops. Lots of ways to do that. Your map, written signs on the subway, signs at the stations along the way, oral announcements (depending on how strong your Japanese is).
11) When you arrive at your final destination, pause again. Look for a map of the area, posted in all subway stations. Tokyo has an extensive underground system of passage ways. Take advantage of them, as they have lots of signs and directions, which you don't have out on the street. Many times, there will be multiple ways to exit a subway station. The exits are numbered and labeled with major landmark (thankfully with English). If you take the correct exit, you are less likely to get lost looking for the place you came to see.
12) When you have to go through gates again, insert your ticket. The machine should keep it if that was your final destination.
13) If for any reason it won't let you out, first try a "fare adjustment" machine. If you look around, you should see one clearly labeled in English. Insert your ticket and see if you have to add any money. Then try exiting again. If that fails, they have attendants on call.

By the way, if you don't want to figure out the fare thing (the hardest part of the whole process), the fare adjustment machines are your best friend. When you buy your ticket, buy it with the minimum fare. When you are getting ready to exit at your final destination, stick it in a fare adjustment machine and add money as required.

Whenever possible, try to get from point A to point B with a single company. It is simpler, and also you will save on fare, as there is a minimum fare that you are paying each time you switch company.

Whenever I go to large cities, I like to learn and use the subway system. It is a quick and fairly inexpensive way to get around. It is also a great place to do some people watching (my favorite activity).

If you are traveling outside of Tokyo (or within), this website can be useful.