I dunno why everyone is talking so much about this. The NDS already has a homebrew N64 emulator. I've used it to play Pokemon Stadium 2 on my R4DS, it's not at full speed but it works. I honestly think the 3DS is more than capable of running N64 games at full speed with an emulator. (if an emulator is made for 3DS mode)
If you'd like proof of this N64 DS Emulator here is a video showing N64 emulation on the NDS :
http://www.youtube.com/watch?v=A6s8prwRumc
Thats not an emulator. Direct from description:
QUOTEI have made a small program which runs along side Win2DS (An NDS VNC client/server) to allow you to play N64 on your DS.
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Note that this is different to an emulator(though it works the same), a proper emulator on NDS is impossible, so this is the next best thing.