I think game-specific resolutions are going to be next to impossible. Just find one resolution you can run your monitor at correctly and just stretch everything to it.
Powerstrip uses application profiles to designate resolutions and such. After you build a profile for a particular application, Powerstrip will automatically apply it when that executable is run, guaranteeing that it'll be run properly. However, you're probably just going to want a static profile to run everything in. Running Windows on an arcade monitor without an ArcadeVGA is complicated enough without having to deal with multiple resolutions.