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.
simavr - a lean and mean Atmel AVR simulator for linux
Solve Elec - Solve Elec is a free educational program to draw and analyze electrical circuits.
SimulAVR - The SimulAVR program is a simulator for the Atmel AVR family of microcontrollers.
Circuit Simulator - Animated electronic circuit simulator using ideal components to visualize voltage and current.