Vin is the voltage powering the arduino. If you hook it up to a 12V power supply the Vin pin will be 12V.
5V is the 5V power coming from the onboard regulator. If you hook up the arduino to a 12V power supply this pin will still be 5V.
If you're using a regulated 5V power supply they're interchangeable, though from my understanding you can use the 5V pin if you want a bit of overvoltage protection or the Vin pin if you need a bit more power (where you're limited by the current limit of the traces, not by the regulator).
It's important to note that both pins are not outputs - you can put power through them as well.
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