You can use that switch in mamewah as a default setting. That way it'll set in at 640x480 for every game and you won't have to fiddle with improper settings.
Of course, this bumps a game's default resolution up to a VGA resolution. If you're bothered by the way the image looks, you can try out advancemame. I haven't messed with it in forever, but it ought to support the same basic MAME switches (like -r 640x480) plus it has some nice built-in video features for "dumming down" the image to make it look more authentic. That's all covered on their website, though.
Hope that helps!