@hacksn5s4 It really depends on what 3DS you have and also what kind of firmware it's got. Right now Gameyob is the closest to perfect on all 3DS systems. However RetroArch is picky with what system it'll run on smoothly.
If you have a N3DS or O3DS with kernel access (which requires you to be on 9.0 - 9.2 on O3DS and not sure on the N3DS) then it will run pretty much fine (O3DS) to flawlessly (N3DS). If you don't have kernel then the worst is O3DS in that case.
If it were me, I'd just stick with Gameyob for the time being. It might have minor sound clicks but it works fine.