Martin Thomas has this nice tool called Evertool in his collection. It is a AVRISP/STK500 and Programmer/JTAG debugger on a single board. It is compatible with AVRStudio with firmware upgrade-ability. So always new devices are supported.
Evertool has following features:
ISP Programmer compatible with Atmel AVRISP, with AVRStudio and avrdude accessibility;
JTAG debugger compatible with Atmel JTAGICE, works with AVRStudio and AvaRice;
All Atmel AVR devices supported with their AVRISP and JTAGICE.;
Easy update of the programmer via RS232/serial port;
Rescue clock generation to recover from wrong fuse-bit-settings;
- Simple hardware, standard parts;
Evertool uses bootloader which is free for non-commercial use. Download latest version from here. Project is very well documented. There are also simplified versions of programmer available like JTAG only debugger, or even Evertool-USB version suggestion. Thomas Martin also has a nice collection of microcontroller programming examples including WinAVR and WinARM which is supported by him.