You should probably store all dates in the database in either your user's local time, or GMT. The server's time zone is irrelevant.
Most of the time you will probably want to store GMT date/time values in the database. This can be accomplished either by using the database function which returns the time in UTC, or getting the date in GMT in PHP in the appropriate manner.
Really, your server should be able to be set to ANY time zone at all and make no difference to your application.
Consider calling date_default_timezone_set on every page request to ensure PHP uses the time zone your users want.
Consider storing all date/time values in the database in UTC if possible, local time otherwise (ignoring the server's clock).
This all presumes that the sysadmins have set the server clock right. If they haven't, raise a support ticket to get it fixed.
Mark