Powering an Arduino with ATX power supply
Neither, I would use the 5VSB supply to the arduino 5V input, this is the standby supply, not the main 5V supply, the PSU fan won't run, neither will the main part of the powersupply, and your power bill will be lower.

If you need to also operate heavy machinery, you could power the that from the main 12V or 5V and control the power-on input to the power-supply from the arduino, only operating the supply at full power when needed.

If this arduino is an accessory to a PC I would use the 5V molex, unless I wanted it to operate duirng suspend and sleep, in which case I would use 5VSB off the ATX main connector, perhaps making the connection using an idc splice connector, or connecting to the power pins of an on-board USB header.