id like to see this go a bit further with lighting support for games that output lights.
Discs of Tron used 2 sets of flashing lights above head, the internal artwork lighting turned off durring the title showing, and i think a few other lights could flash.
Simularly, there were a bunch of other cabs that had light output controllers... like spyhunter - lighting the appropriate 'weapon' from under the artwork...
Im sure that a dev could work with you to help in getting that functionality to work with a device.
Finally, a motor & cylenoid driver would also be usefull too. For use in making replicas of mechanical games like pitch & bat's, pinballs, ice cold beer, ect... and even some video games - Force feedback, ticket output, ect.
In your board design (if you have the outputs) how about a few (3-4) relay contacts. All of the above could be accomplished by just having some dry contacts. Then in your software design, make a "plugin" structure. So then all the great ideas can be accomplished after the fact without a redesign of the board. If relay contacts were included, we could use them for triggering our illuminated translucent trackballs. As long as the relays could be programed like the other LED's ( you said you are working on this) this could be a very cool and functional tool. I would recommend opto isolated relays so different power supplies independent from the board could be used. Heck, I don't know how you are designing your hardware, but if you used relay contacts (or transistors or whatever), anything could be hooked up to your board, not just LED's. And if a music pluggin or attract pluggin were created (as requested above) we could do cold cathode lights, marquee lights, etc... basically anything. With a music pluggin cycling the lights, I can see the BYO jukebox guys latching on to this thing (myself included). Maybe this is beyond the scope of your project but a larger product market is rarely a bad thing. I'm really seeing this thing as really nice light controller, not just a "new Mame button thing". I guess what I'm getting at in this long ramble is make the thing modular and flexible. But hell you should know this crowd... if it can be hacked.. we will do it. If it can't be hacked, we will hack it so it can be hacked

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Also, with all these bright LED's, please keep power consumption in mind. Most of us will be probably powering this off of our pc power supply. A ton of those "you can't look at them" LED's could suck some major juice even though they are LED's. Also some of those super bright LED's require more than the standard 2V that generic LED's most commonly use. A variety of LED's could make a driver circuit a bear. So I guess a question is in order. In your design will the LED's be included, will we be forced to use your LED's, or will we be able to use whatever LED's we have laying around? Or you may not be able to answer this until the board design is finalized.
Whatever board design you come up with, I would like to see screw contact terminals for connections. So we can make whatever wire length our cabinet requires (vertical, sit down, custom etc..). Just like our good ole pal Ipac uses for buttons and such.