Except mess with the bootloader when I didn't quite know what I was doing. Perhaps avrdude/something could test the programmers and ensure they can program the complete memory address range of the device before allowing programming. This would stop or slow down clowns like me from destroying their bootloaders.
I have a Arduino Uno - R3 on it's way and I'm likely to receive it before the real programmer (Atmel AVRISP mkII). I'm considering using as a ISP (eg http://arduino.cc/en/Tutorial/ArduinoISP) and trying to read the flash on the Mega only. But I might just get myself into more trouble with the Uno. The document I've read only talks about uploading bootloader from Uno to Uno.
I really appreciate your time and effort on this Nick, if nothing else hopefully this thread might serve as a cautionary tail for others.