Once upon a very long time ago I used an NES emulator that was able to take the existing synth voices and map them through to the user's hardware synth bank in real time. For the life of me I can't remember the name of that emulator but it would be great if you could incorporate something similar to that in any future patches of Nestopia. If possible, make it so the user can select individual synth voices from their installed synth banks, these would replace, in real time, the NES's individual channels of audio (though I don't think the "Noise" or DPCM channel would work unless they could be made assignable to a percussion synth bank).
I am aware of the fact that many games used one of the square wave channels to produce sound effects, but that's ok. We know how the games sound anyway so it's not that big of an issue especially if this is something that must be toggled under the audio menu.
So in conclusion you'd have whatever the default Windows synthbank is set to i.e. Windows midi mapper, wave table sythn, custom hardware, (even external hardware like a synthesizer) which is toggled to replace the NES sound under the audio menu.
Anyway it's just a thought.
Also, if this has already been addressed, I'm sorry. I couldn't find any information about it.