UTF-8, no doubt. Do everything UTF-8. To put text on UTF-8 on your web page, use it in your HEAD tag:
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
As for MySQL, put the following in my.cnf (config) file:
[mysqld] collation_server=utf8_unicode_ci character_set_server=utf8 default-character-set=utf8 default-collation=utf8_general_ci collation-server=utf8_general_ci
If you get garbage characters from a database from queries made by your application, you may need to complete these two queries before getting Japanese text:
SET NAMES utf8 SET CHARACTER SET utf8
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