Getting There
Air
The main internaional airport is Tokyo's Narita Airport (NRT) but if you're keen to head straight to Kyoto then Kansai International Airport (KIX) in Osaka is a good option. Chubu International Airport Centrair (NGO) in Nagoya also gets flights from Australia, New Zealand, Canada, the USA and more.
Sea
Why not tag Japan onto the end of your Trans-Siberian itinerary? Ferries run from Vladivostok and Fushiki. If you're in China you can take a boat from Shanghai to Osaka or Kobe, Tianjin to Kobe and from Qingdao to Shimonoseki in West Honshu. Ferries also operate between Japan and South Korea and Taiwan.
Getting Around
Air
Domestic flights are a good option if you want to explore some of the islands of Japan, and also if you want to head up to the snow fields of Hokkaido (you can fly from Tokyo to Sapporo).
Rail
Find out how rail travel is meant to be on a bullet train (shinkansen) across Japan. See Japan Railways for information on fares and routes. If you're planning on travelling by rail a lot in Japan then it's definitely worth getting a Japan Rail Pass, a discount ticket that allows unlimited rail travel throughout Japan over a seven, 14 or 21 consecutive day period. You can only buy these outside of Japan as they're only avaiable to foreigners.
Sea
There are four main islands of Japan, and 3000 smaller ones making up the archipelago. It follows that ferries are a well-honed art here. The main routes for tourists are from Osaka/Kobe (on Honshu) to Beppu/Oita (on Kyushu), Niigata on the Japan Sea coast to Otaru/Sapporo (Hokkaido) and Sendai to Tomokomai in southern Hokkaido. For more on ferry travel in Japan see Japan Visitor.
Bike
Japan is good to bicycists — even cycling in Tokyo is no problem thanks to rules that let you bike on the pavements. A good resource for tips and ideas is Japan Cycling Navigator.