Some days i like to check out whats new in the emulation world, and i just happen to come across this little gem, called RxNES, which is a NES emulator, but this time with a little twist, it has customization.
Here's a snipit from the offical site
When the NES draws the original graphics,
check if there are modern graphics which can be put in their place!
RxNES is basically 80 lines of code added to an Open Source NES Emulator within the Unity3D Engine. Unity3D is not required, you can upgrade games with the Standalone Build.
The added code "hashes" the content of the on-screen "Tiles" and comes up with a name for each tile, it then checks a special "Enhancemennts" folder to see if a new 3D Model (.OBJ) and or Texture are availiable to render on top of the old one.
For more info and support their forums are here.