Get in Japan
Citizens of 61 countries and territories, including most Western nations, can obtain landing permission on arrival without a visa. This is usually valid for a stay of up to 90 days, although certain European nationalities and Mexicans are permitted to stay for 180 days if they note a longer stay upon entry. All other nationalities must obtain a “temporary visitor” visa prior to arrival, which is generally valid for a stay of 90 days. The Ministry of Foreign Affairs maintains an online Guide to Japanese Visas . Note that no visa is required for a same-day transit between international flights at the same airport, so long as you do not leave the secured area.
All foreigners (except those on government business and certain permanent residents) at the age of 16 and over are electronically fingerprinted and photographed as part of immigration entry procedures. This may be followed by a short interview conducted by the immigration officer. Entry will be denied if any of these procedures are refused.
Travellers entering Japan for longer than 90 days are required to obtain a Certificate of Alien Registration (colloquially known as a gaijin card) within 90 days of arrival and carry it at all times in lieu of their passport. Those staying for 90 days or less may complete this registration, but they are not obligated to. This card must be surrendered upon exit from Japan, unless a re-entry permit is held.
A customs issue that trips up some unwary travellers is that some over-the-counter medications, notably pseudoephedrine (Actifed, Sudafed, Vicks inhalers) and codeine (some cough medications) are prohibited in Japan. Some prescription medicines (mostly strong painkillers) are also banned even if you have a prescription unless you specifically apply for permission in advance. You may also require permission in order to import drug-filled syringes, such as EpiPens and the like. Ignorance is not considered an excuse, and you can expect to be jailed and deported if caught. See Japan Customs  for details, or check with the nearest Japanese embassy or consulate.
Once in Japan, you must carry your passport (or Alien Registration Card, if applicable) with you at all times. If caught in a random check without it (and nightclub raids are not uncommon), you’ll be detained until somebody can fetch it for you. First offenders who apologize are usually let off with a warning, but theoretically you can be fined up to ¥200,000.
Most intercontinental flights arrive at either Narita Airport (NRT) near Tokyo or Kansai Airport (KIX) near Osaka; a smaller number use Chubu International Airport (NGO) near Nagoya. All three are significant distances from their respective city centers, but are linked to regional rail networks and also have numerous bus services to nearby destinations. Tokyo’s other airport, Haneda Airport (HND), is still primarily for domestic flights but has begun drawing an increasing number of international flights away from Narita.
Just about every sizable city has an airport, though most only offer domestic flights and a few services to China and Korea. A popular alternative for travellers to these cities is to fly via Seoul on Korean Air or Asiana Airlines: this can even be cheaper than connecting in Japan.
Both Narita and Kansai airports are generally easy to get through and not particularly crowded assuming you avoid the main holiday periods – namely New Year’s (end of December – beginning of January), Golden Week (end of April – beginning of May), and Obon (Mid-August), when things are more hectic and expensive.
Japan’s two major airlines are Japan Airlines  (JAL) and All Nippon Airways  (ANA). Delta Air Lines, United Airlines, and American Airlines also operate sizable hubs at Narita, with flights to many destinations in the US and Asia.
There are a number of international ferries to Japan. Except for the ferries from Busan to Fukuoka and Shimonoseki, these are generally uncompetitive with discounted air tickets, as prices are high, schedules infrequent (and unreliable) and travel times long. In roughly descending order of practicality:
Busan-Fukuoka: JR Kyushu Ferry , 092-281-2315 (Japan) or 051-469-0778 (Korea), operates hydrofoil service several times each day, taking about 3.5 hours and costing ¥13,000 one way. Camellia Line , 092-262-2323 (Japan) or 051-466-7799 (Korea), operates a ferry that takes about 8 hours and starts at ¥9000; if overnight, it may stop and wait in front of Busan Port in the morning until Korean Immigration opens. (Compared to most airports, there should be relatively little security hassle on this line.)
Busan-Shimonoseki: Kanbu Ferry, 0832-24-3000 (Japan) or 051-464-2700 (Korea), daily service. 13.5 hours; ¥9000+.
Busan-Osaka: Barnstar Line, 06-6271-8830 (Japan) or 051-469-6131 (Korea), offers thrice weekly service. 18 hours; ¥13,700+.
Shanghai-Osaka/Kobe: Japan-China Ferry, 078-321-5791 (Japan) or 021-6326-4357 (China), thrice weekly service. 45 hours; RMB1,300 from China, ¥20,000+ from Japan.
Tianjin-Kobe: China Express Line, 03-3537-3107 (Japan) or 022-2420-5777 (China), weekly service. 50 hours; ¥22,000+.
Qingdao-Shimonoseki: Orient Ferry , 083-232-6615 (Japan) or 0532-8387-1160 (China), thrice weekly service. 38 hours, ¥15,000+.
Suzhou-Shimonoseki: Shanghai-Shimonoseki Ferry, 083-232-6615 (Japan) or 0512-53186686 (China), thrice weekly service. ¥15,000+.
Keelung (Taiwan)-Ishigaki/Naha: Star Cruises, +886-2-27819968 (Taiwan) or +81-3-64035188 (Japan), , irregular cruises in summer high season only (May-Sep), not available every year. One-way fares generally not available.
Sakhalin-Wakkanai: Heartland Ferry. 5.5 hours; ¥21,000+. Service is suspended October-April due to sea ice.
Russia to Japan via Sakhalin itinerary.
Vladivostok-Takaoka (Fushiki): Far East Shipping Co c/o United Orient Shipping, 03-5640-3901 (Tokyo), roughly weekly. 42 hours; US$320+.