Here is the custom shield I built for the SmartHome central station.
Every Raspberry and ATmega328 pins are broken out, 5v and 3v I²C buses were added, the serial communication could be enabled/disabled with some jumpers, there's also a socket for a optional oscillator and a 3.3v LDO regulator (the ATmega328 actually runs on 3.3v / internal 8MHz).
The ATmega part could be reprogrammed directly from the Raspberry Pi, acting like a serial / SPI programmer. Ultimately, it will be possible to edit and reprogram the chip from the web interface.
This board has been especially designed to be built with a perfboard as I have no way to prototype some PCB : 3 weeks wait time is way too much for a prototype, and I don't own (or have access to) a CNC machine.