- http://www.fpgaarcade.com/ (shipping in very limited numbers; source/schematics have been promised "when ready" but are not available yet)
For both of these the FPGA does the bulk of the work. The Minimig cores have been ported to other boards (including Chameleon, mentioned below, as well as Xilinx dev boards I think). FPGA Arcade is also intended to support a bunch of other machines.
For the C64 and Amiga there's also the commercial C64 Chameleon (http://www.vesalia.de/e_chameleon.htm) that can plug into a real C64 and effectively replace most of it, or work as a standalone unit.