Hey Jeff,
They were using a Raspberry Pi with RetroPie (
http://blog.petrockblock.com/retropie/). The Nintendo joysticks were USB. You can find on Amazon for $8. To my knowledge RetroPie is by far the best interface out there, I'm currently using a different one (PiMame) and and although mine works great the RetroPie UI can't be beat.
As it happens I have a custom built Raspberry Pi arcade here in my office, have a whole bunch of information if you're interested, ping me directly and we can trade notes.
Jason
CodeMash Cofounder