Transportation - JAPAN

Pusan-Shimonoseki
The Pusan-Shimonoseki ferry route is the cheapest route between South Korea and Japan, and no doubt, one of the most popular as well. The Kampur Ferry Service's vessels Kampu or Pukwan leave Pusan at 6 p.m. and arrive in Shimonoseki at 8:30 a.m. the next morning. Availability: Daily
Pusan-Fukuoka
The JK Line Hydrofoil is an ultra-fast hydrofoil service. The journey which takes just three hours costs about US$120 single, and US$220 return.
The Camellia-line ferry service takes around 15 hours from Pusan to Fukuoka at a cost of US$85 single, US$120 return. Availability: Daily
China
There is a weekly ferry service that connects Shanghai to Osaka/Kobe. The ferry's destination alternates each week between Osaka and Kobe. The journey takes two days. A second class ticket on this Japan-China International Ferry Service costs about US$180.
There is another weekly ferry service called the Shanghai Ferry, which connects Osaka and Shanghai. Tickets are similarly priced. There are also ships from Nagasaki to Shanghai every Thursday. Visitors wanting to go to Tanggu (near Tianjin) from Kobe could get on the ship that leaves Kobe every Thursday at noon. The ship reaches Tanggu the following day. Economy and first class tickets cost US$200 and US$300 respectively. You can get your tickets in Tianjin from the shipping office (Tel: 31-2243) at 89 Munan Dao, Heping District. In Kobe, the office is at the port (Tel: 078-321-5791).
Taiwan
Ishigaki, Miyako, Keelung and Kaohsiung. If you are travelling to any of these cities, you can take the weekly ferry service, which operates between Taiwan and Okinawa.
Sometimes, the route goes via Ishigaki and Miyako in Okinawa Prefecture. The Taiwan port alternates between Keelung and Kaohsiung. Departure from Okinawa is on Thursday or Friday; departure from Taiwan is usually on Monday. The trip takes 16 to 19 hours.
Korsakov, Russia to Wakkanai (Hokkaido), Japan
Korsakov is at the very southern tip of Sahkalin Island, which is next to the Russian mainland, but far from either Vladivostok or Khabarovsk. I don't know why you'd want to go there. Wakkanai is at the very far northeast tip of Hokkaido, a very long way from Tokyo, and even very far from Sapporo!
The Higashi Nihon Kai Ferry company runs ferries on this route two or three times a week between early May and mid-October. In July and August they run Monday, Wednesday, and Friday from Wakkanai and Tuesday, Thursday, and Saturdays from Korsakov, but the days vary. They leave at 10:00am from both ends, arriving at Korsakov at 17:30 and Wakkanai at 13:30. (There is a 2 hour time difference). The trip takes 7.5 hours.
The fare is ¥20,000 in second class; ¥25,000 in first; and ¥30,000 in special class. Round-trip fares are just ¥10,000 more for each class.

Vladivostok, Russia to Fushiki (Takaoka), Japan
Vladivostok is on the Japan Sea, near Korea and China and is at the terminus of the Russian section of the Trans-Siberian Railway, at the far eastern extreme of Siberia. It is a one-week train ride to Moscow, leaving every odd-numbered day. Takaoka is not too far from Kanazawa on the Japan Sea coast; the actual destination port is called Fushiki.
The FESCO company runs ferries from Vladivostok Saturdays at 18:00 (6pm), arriving in Fushiki on Mondays at 9:00am. It returns on Wednesdays at 18:00, arriving on Friday at 9:30 am in Vladivostok. [Warning: the Fesco page seems to only work well with Internet Explorer.]
The fare is about ¥28,000 cheapest to ¥88,000 for the most expensive. I don't have any more detailed information at this time. The same company reportedly runs another ferry from Vladivostok to Niigata city.