I completely agree with Kman, as well as the suggestion if you have the funds to support it. That's what I'd do too!
The few reasons I would de-case my PC are:
1. Easier dust clean-up. Dust is going to build-up regardless if your PC is in a case or not, so my logic is that if it's not cased, it'll be easier to get at the components with your can of compressed air.
2. Heat. Inside your cabinet heat will rise, having more room for heat to circulate from it's parts is really beneficial to the longevity of your components. You may say, "but my case has plenty of fans for ventilation". That may be true, but what good is a well vented case, when all it's blowing into it is hot air generated from your cabinet. Without a case, you have more area space for the heat to dissipate.
3. Stability. Unless you drill your PC case to the cabinet, or fasten it somehow, having the PC parts attached right to the cabinet allows for less things moving around inside the cabinet, for when your hulky friends crank on your controls during a heated battle of robotron, shifting the cab around. As well, when you plan to relocate your cabinet to another spot, you don't have to worry about pulling the PC out of the back before moving.
4. It also has a bit more of a professional feeling to it.
These are my reasons, it may not be what you guys care for, but for me I'm pretty set on leaving it out of the case. I like to look at my cabinet and think "this is an arcade cabinet, it's not just a painted box with a PC stuck in it" (even though that's exactly what it is). De-casing it makes the entire cabinet feel like one whole product to me.
Epyx, can't wait to see your pics! I'm assuming you're going to go with them for the marquee as well?