Alliance CAD System is a free set of EDA tools and portable cell libraries for VLSI design. It covers the design flow from VHDL up to layout. It includes VHDL simulator, RTL synthesis, place and route, netlist extractor, DRC, layout editor.
SDBoot is a complete bootloader solution (MCU side and PC side), free, with source code for AVR MCU chip. It features a checksumed protocol for safe programming.