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
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.
SimulAVR - The SimulAVR program is a simulator for the Atmel AVR family of microcontrollers.
PyLab_Works - PyLab_Works is a free and open source replacement for LabView + MatLab, written in pure Python.