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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