Atmega328 board output voltage I'm thinking about making my own "arduino" low power board but I have a question about the atmega328. Is the output voltage on the pins always 5v or it depends on the input voltage I gave to the atmega?

Thanks in advance.
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).