On the Websanova.com site there's a recent post about doing timezones the right way when working with them in PHP and storing them in your (MySQL) database.

Timezones are actually a very trivial concept but they seem to be overlooked and over complicated. [...] Rather than storing a timezone with each date it's better to just accept a standard time to store all your dates with, thus doing the conversion to that standard time before storing the value in the database. It doesn't really matter what time we store it as, but it's generally a good idea to just use UTC+00:00.

They talk a little about what the UTC timezone is for those that may not know and show how to set it as the default timezone for your PHP application (with date_default_timezone_set or updating your php.ini). They also include the MySQL configuration option to set its default timezone and and example SELECT statement for extracting the data back out.