Technology enthusiast and product developer John Sloane has published a detailed account of (in his words) "how Arduino gets from power up to executing my software, a long and involved process whose explanation I found to be widely distributed and not easily forthcoming". To make others' lives easier John has described it in detail, and also working with the microcontroller itself, including fuse bits, the bootloader, uploading code with AVRdude and more.
So what is an EtherMega anyway? Quite simply the most fully-loaded Arduino-compatible board on the market today. Apart from being completely Arduino Mega2560-compatible, it includes full Ethernet interface, a microSD card socket, full USB interface, optional Power-over-Ethernet support and still has a circuit prototyping area with extra I2C interface pins. So if your project is breaking the limits, upgrade to the EtherMega today.