the registry stuff would be in the registry.
And no, deleting the folder from program files won't do anything to the registry.
I don't know exactly what you did with the game to get it screwed up, but if you can't uninstall it and can't play it then I'd try deleting the registy entries and the game folder and then see if you can install it.
I'm guessing the bf1942 registry is something like
(at least that's how it is with bf2) There might be something somewhere else too, not too experienced with the registry.
And if you don't know how to find that just go to start -> run and then type regedit
Also all the profiles and configs etc for the game should be in my documents/bf 1942. Just in case you want to back up those.