Programming the microcontroller and testing the joystick with WinVice and International Karate:
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I recommend a good regulated soldering iron with a 1 mm tip for the SMD parts, like my i-CON 1. The easiest way to solder it is a stereo microscope, but magnifying glasses works, too. But with some practice, the SOP-20 IC needed for this project can be soldered without any magnifying.







































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I built one based on Atmel atmega8 because I don't know very much about Freescale's microcontrollers.
See my site at http://www.retronicdesign.com/
Cheers!
Actually, my design is based on Igor Cesko's design.
Latency is not an issue here. Low speed USB is more than enough for joystick interfacing.
http://old.pinouts.ru/Inputs/ControlPortC64_pinout.shtml
So yes, the Sega Genesis joysticks would work with it, too, see this pinout:
http://pinouts.ru/Game/genesiscontroller_pinout.shtml
But you would have to connect pin 7 to GND to select button A or to +5V to select button B and you won't have button C with my current schematic. So you could play C64 games with a Sega Genesis joystick, but if you like to play Sega Genesis games e.g. in Mame, my schematic would need to be extended, but should be not too difficult.
The pinout of the Atari 2600:
http://old.pinouts.ru/Inputs/JoystickAtari2600_pinout.shtml
So this would work without problems.