Atmel STK500v2 compatible boot loader for Arduino ATMEGA2560.

stk500boot_v2_mega2560.hex

Pololu USB AVR Programmer v2.1

avrdude -V -B 5 -P `pavr2cmd --prog-port` -c avrisp2 -p ATMEGA2560 -e -u -U lock:w:0x3F:m -U efuse:w:0xFD:m -U hfuse:w:0xD8:m -U lfuse:w:0xFF:m
avrdude    -B 5 -P `pavr2cmd --prog-port` -c avrisp2 -p ATMEGA2560 -D -U flash:w:stk500boot_v2_mega2560.hex:i
avrdude -V -B 5 -P `pavr2cmd --prog-port` -c avrisp2 -p ATMEGA2560 -u -U lock:w:0x0F:m

USBasp

avrdude -V -B 5 -c usbasp -p atmega2560 -e -u -U lock:w:0x3F:m -U efuse:w:0xFD:m -U hfuse:w:0xD8:m -U lfuse:w:0xFF:m
avrdude    -B 5 -c usbasp -p atmega2560 -D -U flash:w:stk500boot_v2_mega2560.hex:i
avrdude -V -B 5 -c usbasp -p atmega2560 -u -U lock:w:0x0F:m

USBTiny

This programmer does not support devices with greater than 64KB flash (Atmega1281/1280/2561/2560).