NES Controller Conversion
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I found that aftermarket reproductions of the original NES controller are very common and inexpensive on eBay. I bought a pair and converted them for use with Commodore and Atari systems in July 2009.
Aftermarket NES Controller
The NES cable is removed and replaced with an Atari-style one. Rather than ruin a joystick by cutting off its cable, I picked up a couple of aftermarket joystick extension cables also on eBay. I cut them in half and saved the other half for another project. I routed the new cable in a different way than the NES one, such that it still provided good strain relief but also was at a good angle for the new connections to the board.
Rewired for Commodore and Atari
The aftermarket controller has been cost reduced from the original NES controller. Instead of a chip in a DIP package, it has an epoxy blob on the board. This is not easily removed and there are no convenient holes for the new wires. Due to this, I had to scrape away the solder mask and solder directly to the traces. I secured the wires with hot melt glue.
After Conversion
The finished controller looks just like it was before the modification, only it now has the new cable. The Atari-style plug only supports a single FIRE button while the NES controller as several buttons: A, B, Select, and Start. Rather than have the extra buttons be non-functional, I bridged them so they each work as the FIRE button.
More photos of the conversion can be found in this photo set.