I realize getting around Tokyo probably isn’t a top priority for most people these days, but as I was there recently (before the earthquake) and will be back in a few months escorting some newcomers to the city, I thought it might be a good idea to write down some of my thoughts.
Tokyo has an extensive subway and light rail system (not to mention the superb inter-city trains as well). There is almost nowhere you can’t get to in Tokyo via the subway or the JR (Japanese Rail) lines. It is for this reason coupled with the fact that taxis are extremely expensive, that I highly recommend making yourself familiar with the subway/JR system.
A quick glance at the map (PDF version) can be quite overwhelming, but once you spend a few minutes figuring it out, it isn’t too bad. In particular, it useful to distinguish the JR lines (in particular the JR Yamanote line which circles central Tokyo) from the subway lines as the JR lines run above ground and so switching lines may not be as simple as changing trains inside a station. That being said, as long as you follow the signs, it isn’t too hard to find them from each other. However, I should point out that even connecting between subway lines you might be required to walk quite a distance, exiting and later re-entering the ticket area, and even possibly go outside to get to a connecting line at the same station. A good example of this is at the Kuramae station where switching between the Asakusa and Oedo lines requires leaving the station and walking nearly a quarter of a mile around the block to get to the other line at that same station. There really isn’t a good way to predict this, so just be prepared that not all connections can be made in a timely fashion. That being said, the trains themselves run like clockwork, it’s just the time between trains which is not guaranteed.
If you look closely at the map, you will notice that there are many separate lines which are operated by different companies (with different fare systems) which can make paying for your trip complicated if you don’t have either Suica or PASMO prepaid fare card.
Having one of these cards is invaluable if you want to be able to move around Tokyo easily and without a lot of drama. I would recommend Suica over PASMO as it can be used outside of Tokyo as well as the fact that many stores and restaurants accept Suica as a mechanism of payment (just like using a debit card). There is a very detailed page over at Japan-Guide.com, which is well worth a read, that describes the subtle differences between the cards as well as how to use them in practice.
One issue that is not particularly well covered (in my opinion) by the Japan-Guide.com site is how to actually obtain one of these cards. The site explains that a card can be obtained from one of the many Suica machines (shown on the left) that you will find in every station. However, my experience has been that this is only true for the pink colored machines (not shown) and possibly the blue colored machines as well, but I’m not positive about that. Furthermore, most stations seem to only have the standard green charging-only machines as opposed to the pink or blue dispensing ones. Realistically, your best bet is to get a Suica card right after you land at the airport. The JR ticket office at Narita airport (below) offers a great deal on a Suica card in conjunction with a ticket for the Narita Express. No interaction with machines is required although you may need to point to a picture of a Suica card on the wall in case your Japanese or their English isn’t quite up to the challenge. Apparently, there is a similar deal available to people arriving at Haneda airport for a monorail ticket and a Suica card. I’ve never flown into Haneda so I can’t speak to that experience.
One last thing, while the stations and maps are usually well labeled in English inside the JR Yamanote line, once you get a bit further out, most of the maps become Japanese only. It is well worth it to purchase an subway map in your native language (be sure to get one which includes the JR lines). In addition, it might also be worth learning the Kanji symbols for the important station names on your journey (particularly the one nearest your hotel).