It seems that it does not matter what timezone is on the server as long as you have the time set right for the current timezone, know the timezone of the datetime columns that you store, and are aware of the issues with daylight savings time.

On the other hand if you have control of the timezones of the servers you work with then you can have everything set to UTC internally and never worry about timezones and DST.

Here are some notes I collected of how to work with timezones as a form of cheatsheet for myself and others which might influence what timezone the person will choose for his/her server and how he/she will store date and time.

MySQL Timezone Cheatsheet

Notes:

Changing the timezone will not change the stored datetime or timestamp, but it will select a different datetime from timestamp columns
UTC does not use daylight savings time, GMT (the region) does, GMT (the timezone) does not (GMT is also confusing the definition of seconds which is why UTC was invented).
Warning! UTC has leap seconds, these look like '2012-06-30 23:59:60' and can be added randomly, with 6 months prior notice, due to the slowing of the earths rotation
Warning! different regional timezones might produce the same datetime value due to daylight savings time
The timestamp column only supports dates 1970-01-01 00:00:01 to 2038-01-19 03:14:07 UTC
Internally a MySQL timestamp column is stored as UTC but when selecting a date MySQL will automatically convert it to the current session timezone.

When storing a date in a timestamp, MySQL will assume that the date is in the current session timezone and convert it to UTC for storage.
MySQL can store partial dates in datetime columns, these look like "2013-00-00 04:00:00"
MySQL stores "0000-00-00 00:00:00" if you set a datetime column as NULL, unless you specifically set the column to allow null when you create it.
Read this

To select a timestamp column in UTC format

no matter what timezone the current MySQL session is in:

SELECT 
CONVERT_TZ(`timestamp_field`, @@session.time_zone, '+00:00') AS `utc_datetime` 
FROM `table_name`

You can also set the sever or global or current session timezone to UTC and then select the timestamp like so:

SELECT `timestamp_field` FROM `table_name`

To select the current datetime in UTC:

SELECT UTC_TIMESTAMP();
SELECT UTC_TIMESTAMP;
SELECT CONVERT_TZ(NOW(), @@session.time_zone, '+00:00');

To select the current datetime in the session timezone

SELECT NOW();
SELECT CURRENT_TIMESTAMP;
SELECT CURRENT_TIMESTAMP();

To select the timezone that was set when the server launched

SELECT @@system_time_zone;

Returns "MSK" or "+04:00" for Moscow time for example, there is (or was) a MySQL bug where if set to a numerical offset it would not adjust the Daylight savings time

To get the current timezone

SELECT TIMEDIFF(NOW(), UTC_TIMESTAMP);

It will return 02:00:00 if your timezone is +2:00.

To get the current UNIX timestamp:

SELECT UNIX_TIMESTAMP(NOW())

To get the timestamp column as a UNIX timestamp

SELECT UNIX_TIMESTAMP(`timestamp`) FROM `table_name`

To get a UTC datetime column as a UNIX timestamp

SELECT UNIX_TIMESTAMP(CONVERT_TZ(`utc_datetime`, '+00:00', @@session.time_zone)) FROM `table_name`

Get a current timezone datetime from a UNIX timestamp

SELECT FROM_UNIXTIME(`unix_timestamp_int`) FROM `table_name`

Get a UTC datetime from a UNIX timestamp

SELECT CONVERT_TZ(FROM_UNIXTIME(`unix_timestamp_int`), @@session.time_zone, '+00:00') 
FROM `table_name`

There are 3 places where the timezone might be set in MySQL:

Note: A timezone can be set in 2 formats:

an offset from UTC: '+00:00', '+10:00' or '-6:00'
as a named time zone: 'Europe/Helsinki', 'US/Eastern', or 'MET'

Named time zones can be used only if the time zone information tables in the mysql database have been created and populated.

in the file "my.cnf"

default_time_zone='+00:00'

timezone='UTC'

@@global.time_zone variable

To see what value they are set to

SELECT @@global.time_zone;

To set a value for it use either one:

SET GLOBAL time_zone = '+8:00';
SET GLOBAL time_zone = 'Europe/Helsinki';
SET @@global.time_zone='+00:00';

@@session.time_zone variable

SELECT @@session.time_zone;

To set it use either one:

SET time_zone = 'Europe/Helsinki';
SET time_zone = "+00:00";
SET @@session.time_zone = "+00:00";

both "@@global.time_zone variable" and "@@session.time_zone variable" might return "SYSTEM" which means that they use the timezone set in "my.cnf".

For timezone names to work you must setup your timezone information tables need to be populated: http://dev.mysql.com/doc/refman/5.1/en/time-zone-support.html

Note: you can not do this as it will return NULL:

SELECT 
CONVERT_TZ(`timestamp_field`, TIMEDIFF(NOW(), UTC_TIMESTAMP), '+00:00') AS `utc_datetime` 
FROM `table_name`

Note: According to the docs, the value you set for time_zone does not change, if you set it as "+01:00" for example, then the time_zone will set as an offset from UTC, which does not follow DST, so I assume that it will stay the same all year round.

You can read more about working with DST here

suvozy/MySQL Timezone Cheatsheet.md