It doesn't matter....I'd go 51% with the resistor closer to the Arduino pin. Just for safety's sake, if you mistakenly short something out the resistor has a better chance of protecting the pin from overcurrent. Suppose you mistakenly short out the LED anode to GND. In configuration (4) that you drew you'd be shorting out the Arduino pin and quite possibly damaging the microcontroller. In configuration (3) the pin is protected by the resistor. Of course, you could always short the "wrong" end of the resistor to ground too, so it's no guarantee of anything.....
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The Quick Shield: breakout all 28 pins to quick-connect terminals