so you are looking for bootloaders... huh?
you can search for the arduino bootloader (lurk on the arduino page) it works over the USART (you can use the ft232 to connect to PC or a MAX232 to use a legacy-serial COM...
you can search fo the v-usb bootloaders (more info on the v-usb page ) like the avr USBoot
https://www.fischl.de/avrusbboot/
the one i like very much is the USBaspLoader
https://www.obdev.at/vusb/usbasploader.html because i can use the avrdude to program it....
(there is also a HID bootloader by the v-usb page, it can be useful in Vista an 7 where is a pain to install drivers)
Of course you need to program the bootstrap on the microcontroller the first time (using an available avr programmer)!
if you don't have any (or maybe this is what you are looking) you can use a LPT avr Programmer like the STK-200 (which also can be programmed with avrdude) or the one which @ajishgopalr suggested... these programmers need to be connected to a Legacy port (LPT or COM) not a USB-converter... it will not work this way...