This fully compatible alternative to the Arduino bootloader requires an AVR ISP programmer to burn it to the chip on your Arduino.

Arduino Builder Arduino Builder is a fully standalone utility for viewing, compiling and uploading Arduino sketch file and compiled ELF or HEX file (usually bootloader) to Arduino board with Arduino ...

Anyone who enjoys building electronic projects using the Arduino prototyping and would like to program their own Atmega328-PU chips. May be interested in a new Arduino prototyping kit and ...

With just enough memory to back up the AVR’s flash, the bootloader can shuffle the existing program out to the EEPROM while flashing the new program in. For more details, read the source.