Travel to Japan
・Accomodation
There are several type of accommodations in Japan such as hotels and Ryokan (traditional Japanese inns when you sleep on futon mattress) If you go to small operations, they may not have any bilingual staffs to help you so you may want to confirm there will be no language issue when making a reservations. Don't expect most Japanese can speak English or other foreign language! You should be OK communicating in English if you are staying at big international hotel chains or large local hotels. Most Japanese accommodation quote per person, not per room so make sure to get an estimate of total costs if you are traveling with your entire family.
You can refer to your travel agency or hotel websites to make a reservation of large hotels and ryokans so i would like to list out some of the unique accommodation types in Japan. They are run by small operations so you can not expect staffs are fully bilingual so they are recommended for seasonal travelers in Japan.
Love hotels

Love hotel is very unique type of accommodation for couples in Japan. They are usually located backside of main streets of big city, like Shibuya, Tokyo or around highway interchanges. You can of course spend a night at a love hotel or you can take a rest usually around 2 hours there. As you can imagine, you can take a rest with your partner and have some fun! You can use big touch screen panel to select the type of your fantasy room. The cost is usually between ¥6,000 and ¥10,000 for overnight stay and ¥3,000 and ¥5,000 for the rest. The room is in general clean and pretty private and you can enjoy your room of fantasy such as Hello Kitty.

There are some simple amenities including mini drink bar and some rooms even have karaoke machines! If you are the first time traveler in Japan or traveling with your kids, love hotel is not recommended, but it is very unique accommodation with a lot of fantasy so it's certainly worth exploring it when appropriate. 
Capsule hotels

Capsule hotel is another unique type of accommodation in Japan. The space is quite limited, but you can at least stretch your legs to sleep with relatively low costs. The costs are around ¥3,000 to ¥4,000. The capsule hotels are separated by gender, but you can hardly see women staying at a capsule hotel. Some capsule hotels are equipped with sauna and public bath.
After you enter the capsule, you will use simple control panel to turn on the light and TV. You don't have much space, but you can buy beer and some snacks to enjoy your own time at the end of the day. Although there is not much privacy at the capsule hotels, you may want to experience the night at the capsule hotel. Hope you will not bump into a noisy neighbor with annoying
snore! 
Net cafe
Net cafe is also know as "manga kissa", comic cafe where you can read Japanese comics and use PC to browse website and use on line games. The cost is usually ¥400 for the first hour and additional charge of around ¥100 per 10-15 minutes. Most net cafe is open for 24/7 and offers reasonable night time rate for those who want to stay over night. Night time rate is usually around ¥2,000 to ¥3,000. Soft drinks are offered for free of charge and you can also take light meals with reasonable costs.
Some homeless people is Japan goes to daily labor and spend a night at net cafe as the cost is cheaper and one can take a shower. The place is in general clean and safe as there will always be a few staffs to help customers. Surprisingly, you can see some young women staying overnight at the net cafe. Net cafe is not really an accommodation, but you may want to check out a home of many youngsters who loves Japanese comics and on lineTransportation games.
・Transportation
Most travelers land at either Narita Airport which is close to Tokyo or Kansai International Airport near Osaka. Some travelers may arrive at smaller airport such as Chubu Internationals Airport near Nagoya, Sapporo International Airport, Hiroshima International Airport and Fukuoka International Airport. Haneda Airport which is conveniently located near the central Tokyo is primarily used for domestic flights, but some internatioanls flights from Asia arrive there.

All foreigners at the age of 16 and over are required to take an electronically fingerprint and photograph as part of immigration procedures except those who have permanent residency status or come on governmental purpose. My friend used to complain about this, but it was not as bad as he thought as the traffic was pretty smooth, but you want to get out of the airport as soon as possible as those main international airports may be pretty far away from your final destination of the day! It usually takes me about 2 hours to get home in central Tokyo after landing in Narita so I have to make another small trip after long international flights. I really hope Haneda Airport will be expanded to accommodate more international flights for the sake of travelers and business persons coming to Tokyo.
Get around the cities
Japan is known for very sophisticated transportation system. The trains is the most popular means of transportation and you can expect all trains comes and arrives on time. If you are traveling from city to city, Japan Railways (JR) Shinkansen bullet train is the most popular option. It takes about 2 1/2 hours from Tokyo to Osaka. Once you get to the major train stations, you can take public bus which costs around ¥200 or take a taxi which costs around ¥600 for the first 2km.

Although Japanese transportation system is very reliable, the cost is very very expensive. One of my colleague who are relocated to Tokyo for the first time took a cab from Narita Airport to his hotel in Roppongi, central Tokyo and it costed him over ¥30,000. He didn't think his hotel was so far away from the airport and the taxi costs will be so high. That was his first lesson learned in Japan - the things are very expensive in Japan! 