This seems like something Mahoney might also be interested in doing.

Basically, you set up a computer with MAME (Multiple Arcade Machine Emulator (Runs old arcade games like Paperboy, Missile Command, etc etc), and whatever other emulators you want (I've got NES, SNES, MAME, PS1, and PS2). You get the ROMs and stuff too, and then you get a front-end (My favorite is Hyperspin).

The website I used to buy the buttons and interface is UltiMarc. They are in the UK, but they are incredible. Their prices are average (I spent about $130 including shipping), but their shipping is pretty much the greatest thing ever. I ordered it, the next day, the order starts shipping. The next day, the order arrives at my door. From the UK all the way to Oregon in just a day or 2. Nice.

You buy the buttons and the interface and the joysticks, and then you wire them all up (Pretty simple, just daisy-chain a ground wire through all of them, then hook up each individual button and joystick-microswitch to the interface (I got the i-Pac2, which has 32 inputs (16 inputs for each player)). Then you build the cabinet, or buy one.

In the end, you get something like this: http://www.arcadecabinet.net/wp-content/uploads/2010/08/lowerhell-MAME-Custom-Arcade-cabinet-by-Matthew-Apps.jpg

But it only runs the games you want, from whatever system you want. You could even run PC games with a trackball. Just had a vision of running Red Alert 2 on the arcade machine...

So yeah, I'm in the process of building one now, I'm currently wiring everything up, and you can follow my development a bit more from here (clicky)