Emulino - an emulator for the Arduino platform by Greg Hewgill
KiCad - A Cross Platform and Open Source Electronics Design Automation Suite
simavr - a lean and mean Atmel AVR simulator for linux
Proteus PCB design - Proteus PCB design combines the schematic capture and ARES PCB layout programs to provide a...
SimulAVR - The SimulAVR program is a simulator for the Atmel AVR family of microcontrollers.
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.