N64 case is too small to fit any type of gaming system in there. You may be able to run a simple computer in the case, just get a full board with built in CPU and video card. Although you said an "emulator" so I'm guessing to run old games in ROMs? You don't need a good video card for that.
Like this http://www.newegg.com/Product/Product.aspx?Item=N82E16813157228http://www.newegg.com/Product/Product.aspx?Item=N82E16813500065
And a power supply for a gaming system will be the size of the N64 give or take, so no room for anything else. For a small system to run old 8-bit games on, should have no issues with a low end CPU and video card.