On one server, when I run:
mysql> select now();
+---------------------+
| now() |
+---------------------+
| 2009-05-30 16:54:29 |
+---------
If you are using the MySql Workbench you can set this by opening up the administrator view and select the Advanced tab. The top section is "Localization" and the first check box should be "default-time-zone". Check that box and then enter your desired time zone, restart the server and you should be good to go.