Cr0sh is right on the money - again :). I use the Arduino for working out a sketch, breadboarding to get the project working. Once it's to where I want it (still gets changed at least twice more) - I will layout a PCB for the m168 chip, usually a LCD display, then build a complete stand alone board.
The final m168 chip the hex file created by the Arduino IDE burned to the chip using Studio4 and an external programmer, hence loosing the bootloader.
Your imagination is the limit 
Ken H>