In my travelogue about heading to the Silk Road, I included some advice about travel and living in Japan, Korea and China so I thought I would gather them together in this post along with some additions.

The Nihon-kai (Japan Sea) Sleeper Train / Related post
The Nihonkai is the sleeper train that runs between Aomori (the northen most prefecture on the main island of Japan - Honshu) and Osaka along Japan Sea coast – passing through the prefectures of Akita, Yamagata, Niigata, Toyama, Ishikawa, Shiga and Kyoto. This train runs both ways twice a day. B-sleepers (B-shindai), which have cabins with upper and lower beds and storage above the corridor are the cheapest. They isn't a restaurant cars, so you should take some snacks or food with you.
Aomori ~ Osaka: 14 and half hours / ¥21740 (about US$186)

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Useful Japanese railway ticket: Seishun 18 Kippu (ticket) / Related post
Most foreign travellers to Japan know about The Japan Rail Pass, but if you want to travel more cheaply by train in Japan then the Seishun 18 Kippu might just be for you.
This lets you can take local (futsu普通 or kakueki各駅 in Japanese) and rapid (kaisoku快速 in Japanese) trains for any 5 days during the school holiday for only 11500 yen (less than US$100) anywhere in Japan on JR lines. Be careful though as there are a number of railway operators in Japan and this ticket is only valid on JR lines. Local trains in Tokyo and the Osaka area are always crowded, but once you escape from the city, you can relax and enjoy your train journey. You can also take rapid night trains, which run specially during school holidays. If you want to take these trains, you will need to make a reservation.

*Moonlight Nagara (daily): Tokyo - Nagoya - Ogaki (near Kyoto)
*Moonlight Echigo (daily): Shinjuku (Tokyo) - Niigata
*Moonlight Kyushu (daily during school holidays):
Shin-Osaka (Osaka) - Hakata (Fukuoka, top of southern island)
*Moonlight Matsuyama (daily during school holidays):
Kyoto - Matsuyama (Ehime, western Shikoku island)
*Moonlight Kochi (daily during school holidays):
Kyoto - Kochi (southern Shikoku island)
*Moonlight Shinsyu (mainly every Friday during school holidays):
Shinjuku - Hakuba (northern Nagano, famous for ski fields near Tokyo area)
*Gelande Zao (every Friday during school holidays):
Ofuna (Kamakura, near Yokohama) - Yamagata (northern Honshuu, famous for good ski fields)

In the middle of August, over New Years and when some big events are on, like summer rock festivals such as Fuji Rock, in the countryside or Comi-ke (comic markets - anime geek events held every summer and winter) in Tokyo, the trains will probably be booked out, so if you can, you should book early. You can book up to one month in advance. Timetable search engine

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Ferries from/to Japan / Related post
Japan National Tourist Organization
Japan Cycling Navigator

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Ferry between Osaka and Pusan, Korea: Panstar Ferry
(No English website / Japanese website) / Related post
Operated by a Korean company.
From Osaka: 16:00 on Mon, Wed, Fri
From Pusan (Busan): 16:00 on Tue, Thu, Sun
Docks at 10:00am the next day.
*Booking Phone Numbers:
Osaka:+81-6-6271-8830
Seoul:+82-2-775-6811
Pusan:+82-51-462-5482

The ferry terminal in Osaka is located near the Cosmo-Square station on the Chuo subway line.
You can take a free shuttle bus from the station to the terminal from 11:20am to 2:20pm.
The cheapest ticket - Standard Room costs ¥13700 (about 117US$) one way. Return tickets are discounted 20%, Student discount is 20%, and online booking discount is 5% (you cannot pay by credit card if you book on line).

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Ferry between Kobe and Tianjin, China: Yanjing Ferry (English website)
/ Psymeg took this ferry to China.
Run by a Chinese company.
From Kobe: 12:00 every Friday
From Tianjin: 11:00 every Monday
Arrives at 2:00pm on the second day after the day of departure.

This company is more serious than the Panstar Ferry Company, like their website, booking reply etc. Please check the website in detail. Lots of interesting pictures of the ferry, like heaps of empty beer bottles on the deck, can be found on the company blog (in Japanese)