KiCad - A Cross Platform and Open Source Electronics Design Automation Suite
AVRDUDESS - AVRDUDESS is a GUI for AVRDUDE, a tool for programming Atmel microcontrollers.
Proteus PCB design - Proteus PCB design combines the schematic capture and ARES PCB layout programs to provide a...
avrdude-gui - a GUI Interface for the popular avrdude program.
QUCS - Qucs, briefly for Quite Universal Circuit Simulator, is an integrated circuit simulator which means you are able to setup a circuit with a graphical user interface (GUI) and simulate the large-signal, small-signal and noise behaviour of the circuit.
Khazama AVR Programmer - GUI application for USBasp and avrdude. It can burn data to both flash and eeprom, in addition to programming the fuse bits.