If the cost of shipping your belongings abroad has left you some savings at the end of your stay in Japan, you will want to transfer some money to your new country. The most common way to transfer money is to use a wire transfer (SWIFT) offered by most major banks but only in there main branches (ie often only in the Tsukuba Centre branches). Typically such transfer cost around 3000 yen and the recipient of the transfer will have to pay around 2000 yen of fees.
Carrying your cash in yen abroad and then exchanging may not be a solution either as the fees on cash exchange are often very high.
One cheaper solution might be to open a postal account (giro) in Japan and in the destination country and then to make an "ordinary transfer" from postal account to postal account. For such transfer the charges are only 400 yen!
You can find more details on the postal transfers at http://www.yu-cho.japanpost.jp/e_s0000000/ssk20000.htm.
Lloyds seems also to have good deals:
Here are a few advices on how to ship your belongings abroad.