o2|3DS? NES Virtual Console injections, VirtuaNES or maybe QuickNES (RetroArch).
New 2|3DS? FCEUmm (RetroArch), NES Virtual Console injections or QuickNES (RetroArch) if you want less input lag on supported games.
Personally, I use VirtuaNES for loading ROMs and VC injections when I want to have that game on my o2DS menu.
And, in my n3DS, FCEUmm for loading ROMs and VC injections.