I think the generic file type is ZIP or RAR. It's when people take a large collection of images inside of a single folder and do this crazy thing called compressing files. Weird, I know.
Also, if you lock down your game when you export it, your images won't be seen and your game can't be edited. Only the audio will remain seen, so the least you could do is set a file naming convention for your audio tracks in your game (only the non-rtp ones).
Other than all that, I don't know why you care. VX and XP, and probably 2k3 all have excellent file management.