I had some spare NES game carts lying around and I had been thinking of doing this for a while.. pulled apart the cart did some measurements and found I could fit my Western Digital portable HDD inside. (with some mods to the case internally)
You will need a grinder/dremel to grind out the plastic lugs that support the centre of the cart and other various little tabs inside.
The sides will need a little tweaking as well, but its only a little shave off the sides.
The internal game board will need to have a couple of mm shaved off the top of the board, but it still works once you put it all back together. Infact its pretty awesome to still have the game work while giving you more functionality.
When you go to close it up for the final time once you have everything fitting, you will need to superglue the top corner where you have the USB coming out, normally there is a clip there and now it won't hold together properly without glueing it down.
Any questions, feel free to ask!
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