Yeah, I'm working on a similar project, but I am just going the PC-in-a-cab route... having an actual Arcade PCB with a custom game would be cool, but how to do that? Cheffo's link is probably your best bet. D2K is an example, but it is not an original game, just new levels and some tweaks using existing game resources (not that the creator isn't a frickin' genius). Hopefully soon I will have a blog up about my project... once I get a couple other cabinet builds squared away. What kind of game you thinking about?
eds- I am using gamemaker too! Can't wait to see what you are working on!