Uisp

From Wiki

uisp is the "micro in-system programer" program that can be used to send a binary image to an AVR device. It supports many programming boards, like the STK500 and avrdude. uisp can also be used to do things like erase and verify FLASH memory, set Fuse Bits on the AVR, and other chip configuration parameters that cannot be set from a running program.

UISP Supported programming boards
AVReAl / FBProg
AVRDUDE
STK500 & STK550
STK200 & STK300
Dontronics DT006
As well as a few other "Direct connect" modes, like direct serial & direct parallel. The uisp homepage has more details.