Atmega328 board output voltage
It depends on the input voltage you give it.  If you run the ATMega328p at 3.3V then you get 3.3V out.  If you run it at 5V you get 5V out.

A word of caution about running at lower voltages:  The chip can't run as fast when it has a lower supply voltage - that's why you will see the 3.3V Arduino boards running at 8MHz (or 12MHz at a pinch).