This is all about bootloading for the Atmega 328. Often, many issues come about when bootloading and these quick fixes have been found to be effective for ‘no-wait” and “no-hang” fixing. Changes though have to be made to the ISP tools and its definitions. Also corrected using the bootloader is the constant missing signature bytes issues when trying to program without IDE use. EEPROM codes can also be repaired, including the memory and flash programs. You can also utilize upload feedback options with the LED, but this is reserved for original Arduino systems. The program can easily be inputted when programming, though there are some pitfalls that need to be avoided. This happens when using a Diecimila and its auto reset functions that can accidentally trigger the bootloader because of the inherent system design. And there’s the ever-reliable AVRDUDE to be able to program the Arduino, but you need to know how to use it to make it work. Do plug it into your system using a USB outlet and reset the system before running AVRDUDE.

SOURCE: http://www.ladyada.net/library/arduino/bootloader.html