KiCad - A Cross Platform and Open Source Electronics Design Automation Suite
Emulino - an emulator for the Arduino platform by Greg Hewgill
EasyEDA - EasyEDA - Web-based EDA suite; runs in browser.
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.