VirtuaNES, Snes9x, Picodrive, and TemperPCE (all bubble2k16 ports) work great on o3ds and excellent on n3ds, mGBA works best on n3ds if you don't want to use NSUI Beta 27 for GBA VC injections and also works great for GB/GBC and can do SGB Borders and Palettes, Pokémini3ds for Pokémini emulation works on all 3ds/2ds consoles, Handy3ds (I believe that's what it's called) is an Atari Lynx emulator for 3ds and works decently enough, and retroarch for just about everything else really (works best on n3ds), there's a new Virtual Boy emulator that might still be in development but I haven't kept up with it so I'm not sure
Edit: development of said new VB emulator sadly seems to possibly be dead as there hasn't been updates for a while