В Xubuntu 12.04 я просто добавил
[mysqld]
character_set_server = utf8
в /etc/mysql/my.cnf
И результат
mysql> show variables like "%character%";show variables like "%collation%";
+--------------------------+----------------------------+
| Variable_name | Value |
+--------------------------+----------------------------+
| character_set_client | utf8 |
| character_set_connection | utf8 |
| character_set_database | utf8 |
| character_set_filesystem | binary |
| character_set_results | utf8 |
| character_set_server | utf8 |
| character_set_system | utf8 |
| character_sets_dir | /usr/share/mysql/charsets/ |
+--------------------------+----------------------------+
8 rows in set (0.00 sec)
+----------------------+-----------------+
| Variable_name | Value |
+----------------------+-----------------+
| collation_connection | utf8_general_ci |
| collation_database | utf8_general_ci |
| collation_server | utf8_general_ci |
+----------------------+-----------------+
3 rows in set (0.00 sec)
Также взгляните на http://dev.mysql.com/doc/refman/5.6/en/charset-server.html