I can't answer that, there are too many options.
The ATmega8 16MHz is Arduino compatible, if you use an external X-tal of 16MHz.
The ATmega8L 8MHz is not default compatible, but you can add it to the file boards.txt
Do you want to use a X-tal on the proto-board ? Or do you want to run it at the internal clock ?
Using the internal clock is not very accurate and a serial connection can have a slightly different baudrate.
A standalone Arduino compatible setup, http://arduino.cc/en/Main/Standalone
This is Nick Gammon his page about a compatible setup, http://www.gammon.com.au/forum/?id=11637
You can use an Arduino as a programmer, http://arduino.cc/en/Tutorial/ArduinoToBreadboard