Emulino - an emulator for the Arduino platform by Greg Hewgill
LTspice - LTspice® is a high performance SPICE simulation software, schematic capture and waveform viewer with enhancements and models for easing the simulation of analog circuits.
SimulAVR - The SimulAVR program is a simulator for the Atmel AVR family of microcontrollers.
Proteus PCB design - Proteus PCB design combines the schematic capture and ARES PCB layout programs to provide a...
simavr - a lean and mean Atmel AVR simulator for linux
Pspice - OrCAD PSpice technology provides the best, high-performance circuit simulation to analyze and refine your circuits, components, and parameters before committing to layout and fabrication