I spent easily over 100 hours getting all the game packs working with the arcade-in-a-box. I worked very closely with Tom at GameEx and together we got them working well.
Many of the packs we had to use scripts to remap keys on launch. Others, like the Taito and Namco packs, use automated scripts that launches the software's frontend, then automatically scrolls to the game you selected from GameEx and selects it. It's all automated and does not allow any user input during the time. The midway packs were fairly easy to figure out how to launch specific games from a command line. Same would be true with Namco, but weird things happened when we did it that way.
It was a huge amount of time getting them all working. But now, all the games show up in GameEx in one list (like if you were using MAME) with screenshots/movies.
I will also note that I did talk with the Midway Lawyers and they had no problem with what I was doing with their game packs. As long as I made it clear that any support should go through me and not midway.
I also chatted with Aaron Giles a lot when I doing all of this. Since the Taito packs do use mame, it MIGHT be ok to use mame with those roms since that is how they are packaged on the CD. However, he still wasnt' completely sure about that. He did say that just because you have the Midway pack, for example, you can't just install mame and run the ROMs of the games that come on that pack.
I researched this to death for months and months

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You can also reseach PC games that work with your systems as well. I did that approach for a while with
www.iRetroGames.com If anyone wants to take over that project I would be more than happy to give it up. I don't think I have touched the website in at least a year. It was very time consuming to research games and find ones that would work well with an arcade setup.