I'm not sure the question was understood and answered properly, so I'll throw in my voice.
You asked about not just NES, but across the site? If I'm reading correctly, you also mean the DVD cased games for newer consoles? They're sized to normal dimensions. As are the Gameboy and DS cases, but that's likely a given.
But yeah, everything that's a cart is fit for the universal case, because they rock. But I suppose it really wouldn't be difficult for one to download and alter them to original box dimensions.
Of course, if I misunderstood the question and it's already been answered, I look like a shmuck, but aw well.