bootloading.txt

connection diagram here
http://arduino.cc/en/Tutorial/ArduinoISP
note: connect D10 directly to reset line, with no cap between!

fuses:
328: L:FF H:DE E:05 (FD)
88: L:FF H:DD E:04 (FC)
the enabled ones are for:
enable BOOTRST (boot from bootloader)
and set bootloader size to 256 words (512 bytes)

then, program like this:
/opt/arduino-1.0.5/hardware/tools/avrdude -C/opt/arduino-1.0.5/hardware/tools/avrdude.conf -patmega328 -cstk500v1 -P/dev/ttyUSB0 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0x05:m -Uhfuse:w:0xde:m -Ulfuse:w:0xff:m -v -v -Uflash:w:/opt/arduino-1.0.5/hardware/arduino/bootloaders/optiboot/optiboot_atmega328.hex

if it complains about not knowing about the atmega328, just copy the configuration for the atmega328p, and change the signature to 0x1e 0x95 0x14; this is already in the avrduderc file, which can be used by doing
ln -sf ~/Dropbox/ee/avrduderc ~/.avrduderc


Note: for my programmer, I increased the baud rate to 57600 (this speeds programming from about 30s to 17s; higher baud rates seem to have issues), so you need to change the baud rate in the above command.  updated command:

/opt/arduino-1.0.5/hardware/tools/avrdude -C/opt/arduino-1.0.5/hardware/tools/avrdude.conf -patmega328p -cstk500v1 -P/dev/ttyUSB0 -b57600 -e -Ulock:w:0x3F:m -Uefuse:w:0x05:m -Uhfuse:w:0xde:m -Ulfuse:w:0xff:m -v -v -Uflash:w:/opt/arduino-1.0.5/hardware/arduino/bootloaders/optiboot/optiboot_atmega328.hex

for the ATmega88 (part is different, fuses are different, bootloader hex is different)
/opt/arduino-1.0.5/hardware/tools/avrdude -C/opt/arduino-1.0.5/hardware/tools/avrdude.conf -patmega88 -cstk500v1 -P/dev/ttyUSB0 -b57600 -e -Ulock:w:0x3F:m -Uefuse:w:0x04:m -Uhfuse:w:0xdd:m -Ulfuse:w:0xff:m -v -v -Uflash:w:/opt/arduino-1.0.5/hardware/arduino/bootloaders/optiboot/optiboot_atmega88.hex
- note, may need to compile the 88 bootloader; just go to the optiboot directory and do
PATH=/opt/arduino-1.0.5/hardware/tools/avr/bin/:$PATH make atmega88