I've managed to burn an Arduino style bootloader onto my atmega1284p using a Dragon in jtag mode. I set the fuses for full swing oscillator (0xf7,0x9e, 0xfd). The bootstrap disables the jtag to allow all pins to be used.
The Arduino circuit connects the DTR line of the FTDI usb/serial chip to the reset of the processor though a 100nf cap. The reset line is pulled high via a 10k resistor. This scheme allows avrdude to reset the processor to enter the bootstrap. I've had this work with atmega328's and atmega2561's (it works on the Arduino mega boards that use the atmega2560 and atmega1280 procesors). However is does NOT work on the atmega1284p. I wonder if something is screwy with the reset circuit on this processor. (Grounding the reset line manually DOES reset it, and allow the bootstrap to run. But that takes three hands!)