Citizens of the European Union/EFTA, Andorra, Australia, Argentina, Bahamas, Canada, Chile, Costa Rica, Dominican Republic, El Salvador, Guatemala, Honduras, Hong Kong, Israel, Macau, Macedonia, Mauritius, Monaco, New Zealand, San Marino, Singapore, South Korea, Suriname, Tunisia, United States/American Samoa, and Uruguay can visit visa-free for up to 90 days. Citizens of Brunei can visit-visa free for up to 15 days.
Citizens of Austria, Germany, Ireland, Liechtenstein, Mexico, Switzerland, and the United Kingdom can apply for a extended stay of 6 months with Japan's Ministry of Justice.
Citizens of Barbados, Lesotho, Malaysia, Serbia, and Turkey can visit visa-free for up to 90 days with a biometric passport only. And only 15 days for citizens of Thailand.
Citizens of Taiwan can visit visa-free for 90 days is the passport includes a personal identification number.
Citizens of Indonesia with a biometric Indonesian passport who've been issued a Visa Waiver Registration Certificate from the Japanese Embassy or Consulate in Indonesia can visit visa-free for up to 15 days.
Citizens of China traveling via cruise ships do not require a visa, but must leave and get back on the same cruise ship in order to qualify.
The most common intercontinental flight destination is Narita Airport NRT which is about an hour east of Tokyo. Tokyo's Haneda Airport HND, while still primarily for domestic flights, has recently completing an expansion which has allowed for more international service, so many flights to this, more convenient, airport are also now available. There is a third airport north of Tokyo, Ibaraki IBR which is attempting to focus on discount carriers, but it has not yet attracted significant traffic.
The second most common destination is Kansai Airport KIX about an hour south of Osaka. Osaka International Airport ITM, commonly referred to as Itami airport, is primarily a domestic airport, but it is often cheaper and/or more convenient to connect to Itami rather than Kansai.
A smaller number use Chubu International Airport NGO near Nagoya.
Fukuoka Airport FUK, Naha Airport OKA, and New Chitose Airport CTS also have significant international traffic, but it is primarily to larger cities in the region.
Just about every sizable city has an airport, but most are focused on domestic flights with only occasional service to Korea or China. 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.
Narita, Haneda, 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. ANA offers domestic connections for Star Alliance carriers, and JAL offers domestic connections for OneWorld carriers. There are no domestic connections for SkyTeam carriers, so in this case, you may want to consider a discount domestic carrier.
There are a number of international ferries to Japan, but for a casual traveller, Busan is likely to be the only practical destination from which to take a boat to Japan. Except for the ferries from Busan to Fukuoka and Shimonoseki, boats are generally uncompetitive with air fares, schedules can be infrequent and unreliable, and travel times long. Unless you’re travelling with cargo, spending two days on a ferry is likely not practical.
In roughly descending order of practicality:
Busan-Fukuoka: JR Kyushu Ferry (http://www.jrbeetle.co.jp...), 092-281-2315 Japan or 051-469-0778 Korea, operates hydrofoil service several times each day, taking about 3.5 hours. Base fare is ¥13,000 one way, but discounts down to ¥8,000 round trip are available with advanced purchase (http://www.jrbeetle.co.jp...). Mirajet offers a sister service based in Busan, and reservations are generally valid for either company. Camellia Line (http://www.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: Kampu Ferry (http://www.kampuferry.co....), 083-224-3000 Japan or 051-464-2700 Korea, daily service. 12 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; CNY1,300 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, +81 83 232-6615 Japan or 0532-8387-1160 China, thrice weekly service. 38 hours, CNY15,000+.
Suzhou-Shimonoseki: Shanghai-Shimonoseki Ferry, +81 83 232-6615 Japan or 0512-53186686 China, thrice weekly service. CNY15,000+.
Keelung Taiwan-Ishigaki/Naha: Star Cruises, +886-2-27819968 Taiwan or +81 3 6403-5188 Japan, (http://www.starcruises.com), irregular cruises in summer high season only May-Sep, not available every year. One-way fares generally not available.