Harajuku: Its reputation may have preceded it. Possibly, you've heard Gwen Stefani's "Harajuku Girls" or have just heard the term. If Shibuya is for the early-twenties age set, Harajuku is for pre-teens and teens. The fashion you will spot here is like nothing you will see anywhere else. This is, far and away, the best place to people watch. Harajuku is also a good stop to check out the oldest shrine in Tokyo: the Meiji Shrine. The very old forested grounds and peaceful atmosphere are quite a contrast to the spunky, colorful area near Harajuku station. Americans, take note: Harajuku station is also the end point of Omote-Sando street. This is my favorite street in Tokyo! It's a long, wide, tree-lined avenue full of shops with the best holiday present shopping you will find anywhere (the stores actually take credit cards!)

Shinjuku: If Tokyo has a "Downtown Area", this is it. These are the "tall" buildings you will see from observatories elsewhere around the city. The building pictured above is the unique government building, one among many others. This is the commercial and financial center to end all others and has quite a night life I'm told. Here, you will find movie theatres (even an IMAX theatre, squeezed in on one of many floors of giant buildings), restaurants, CD shops with all the music you can think of, ample Starbucks for your coffee craving, and a Kinokuiya, the best bookstore for a foreigner. And, to top it all off, one of the largest and most beautiful gardens in the city. Shinjuku is dense and easy to get lost in, but worth a wander.

Ikebukuro: This is another fun mini-metropolis of Tokyo with lots of shopping and wandering potential. I note this place in particular because of the 8-storey "Animate" that anime fans may appreciate. It is half a block from "K-Books", the best used manga and doujinshi (and even anime soundtrack) shop you'll ever find.

Japan is a clean and orderly place. True, Tokyo is drab and gray in a lot of places, but always scrubbed clean. The saying here is not "The customer is always right", it's that "The customer is God." Service nearly everywhere, even McDonalds, is fantastic. Are You Being Served? The answer is a resounding Yes. Although there are huge crowds, people are not pushy. Folks queue up patiently when getting on a train or waiting in line. Jaywalking is a rarity. Also, and this may be related to the cleanliness, you will not see people eating while walking. I always wanted to grab a snack or drink to have while I was walking, but it is not considered polite (with the possible exception of ice cream). Despite the overwhelming amounts of vending machines everywhere, you are expected to hang out by the vending machine, consume your beverage, then recycle it on the spot.
Money: Japan is very much a cash-based society. You cannot expect to get around with a credit card or ATM card alone. (You can't even really be sure in finding an ATM that will take your card. Tokyo is the easiest place in Japan to do this - look for ATMS in post offices - but I had an easier time in Beijing...) More and more places are taking cards, but it is better just to carry big wads of cash around like the Japanese do. (Checks are virtually unheard of.)
Hotels and Hot Springs: There are western style hotels, which will look like any hotel in the world (just smaller) and will have ample English speaking employees and a tolerable Western-style breakfast. Then there are Japanese style which will have almost no English, involve sleeping on a comfortable futon on the tatami floor, have sliding doors and the weirdest, fishiest breakfast you will ever eat. But the latter will always have phenomenal service. Both run the range of prices (I've stayed in skeezy and fancy-schmancy versions of both.) See my section on Ryokans (Japanese Inn) for more details; it's an experience I highly recommend. Hot springs are also a lot of fun, relaxing, and are usually elaborate - but be prepared to be nude! Men and women are separate, but there ain't no bathing suits around here. Be sure to shower at the shower station before entering.
Public Toilets: There are two questions you have to ask yourself regarding public toilets in Japan. 1. Can you squat? and 2: Do you need toilet paper? If the answer to the first question is "No", then your best bet is to do what I did: go to the third floor of a fancy department store or go to McDonald's. The newer the place you are, the more likely they will have a Western-style option in addition to squat-style. (And not only will they have a Western-style, but it might be a crazy high-tech toilet with all sorts of buttons for bidet and a mist!) Many places have both, so you just have to check the stalls. Restrooms in nicer places are quite clean and stocked and not too hard to find usually. The answer to your second question is probably "Yes" so if you get stuck in a REALLY public restroom, like at a subway station which will ONLY have squat style available, then you need to carry your own toilet paper. Luckily, the Japanese make this easy! You may see people in front of stores handing out advertisements. More often than not, these advertisements are on tissue packets! Free toilet paper! Grab some! (Also useful for wiping sweat after a long day walking on a humid summer day.) If you are new to squatting, the key trick is to bring your pants down to your knees and hold them there between your knees when you squat. This keeps your pockets upright and your clothes safely dry. And try to relax your weight on your calves instead of burning out your quads; feels a bit weird at first to sit so low, but it is a pretty natural position.
Transportation: Subways and trains go just about everywhere you need and run quite often. The machines may be a little weird at first because they are entirely in Japanese. Basically, if you can find the correct price to where you are going on the map, you can buy the correct ticket just by looking at the numbers, but be careful not to look at the child's price. (The kind of machine that confused me the most had an unlabeled long row of black buttons. What I did not realize was that they lit up with prices once you put money in.) But once you get the hang of them, they are quite quick. Put your ticket through the turnstile and keep it until the end of your ride. It will get eaten at the other end. However, note that many subways stop for the night somewhere around midnight. Taxis are your only option then. Hands down, the strangest things about taxis in Japan is that you do NOT OPEN THE DOOR. The back door of a taxi cab opens and closes automatically. Also, don't assume the driver has any idea where he's going. Other than that, taxis are not a bad option.
Restaurants: Restaurants are plentiful and delicious in Tokyo. You do not need to tip. Most restaurants have full-sized table and chairs or booths, others will have floor tables with cushions. You probably won't have to take your shoes off, but if you are in a more traditional or fancy place, just look for foot lockers near the entrance. You probably won't have to ask for a fork. (If you are obviously a foreigner, you are more likely to have to ask for chopsticks ("o-hashi") if you want them.) Ramen is GOOD here, don't be fooled by your memory of cheap Top Ramen. Prices are almost always in arabic numerals, not Japanese, so that makes it easier. Wax food displays are your friend - many Japanese restaurants have these as a matter of course and it makes knowing what you are about to order SO much easier. At familiar fast food restaurants, the meals are pretty much the same, just the accent is different. You may want to order a "cheezubaagaa." Although the chicken and burgers are good, I don't recommend pizza in Japan, even with an octopus topping.
Bookstores: Japanese newspapers, novels, and manga are backwards from America. You open "from the back" and read right to left. But textbooks and other books read the same as ours, left to right. The way to tell the difference? If the text is vertical, you read it "backwards" otherwise, it's forward. Standing and reading an entire book or magazine in a bookstore in Japan is not only acceptable, but they have a word for it: tateyomi. Only the largest stores will have an English section (Kinokuniya - a chain - is one of the best and has a fantastic selection for books on learning Japanese and taking the Japanese Proficiency Test.)
Movies: Going to the cinema in Japan has the most bloated prices you will see in an already expensive country. In the 90s, the going rate was 1500 yen to catch a flick. I think it has topped 2000 yen (about USD$20) now. The main reason for the expense, I imagine, is the real-estate that theatres take up. You will usually find movie theatres on different floors of tall buildings. Sometimes, they have a special reserved section if you want to pay more. I would estimate that 40% of the movies available at a given time are from the U.S. If the movie was originally in English, it will almost always still be in English with Japanese subtitles. The only ones that you will have to be careful of are kids movies, since those are likely to be dubbed. (Or any movie that has a good portion of it in another country. I was lost the first ten minutes of U-571 since it was in German and normally would have been subtitled in English, but noooo.)
Umbrellas: Carrying one at all times (especially in Tokyo) is not a bad idea since it is known to sporadically rain. The problem: everyone else carries umbrellas, too. Maybe raincoats are not fashionable? Once, I was umbrellaless in Akihabara (starring Tom Hanks) and it started to rain. It was so crowded that I managed to stay dry by threading through all the other umbrella-carrying people. Note: if you are shopping in the rain, look for a funny little stand near the entrance with long, plastic things hanging. You put your umbrella down through the top and it will come out in a nice umbrella-sized plastic bag so you don't get any items wet while shopping. Confused? Watch other patrons do it first.

One evening, I got roped into participating in random festival event (where I got to carry a "mikoshi", a mini-shrine, around town). It was very much like the one in the photo above, which happened right in the middle of a busy street! My co-workers were trying to convince me how special catching the above event was, though, as far as I could ascertain, such things happen quite often in Japan. That was definitely not the last time I saw such a spectacle.