Emus for 3DS
VirtuaNES a high compatibility NES emulator for your old 3DS or 2DS. It's not as accurate as FCEUX or Nestopia, but it runs at full 60 FPS for almost all games, and supports tonnes of mappers: MMC1,3,5,6; VRC1,2,3,4,6,7; and tonnes of other mappers. As a result, the library of games it supports are huge.
This 3DS version also fixes a few bugs from VirtuaNES's MMC5 mappers and even plays Rockman 4 Minus Infinity and Zelda Legend of Link hacks.
TemperPCE (TurboGrafx / PC-Engine) core
This is a port of Exophase's Temper (TurboGrafx/PC-Engine) emulator to the old 3DS and old 2DS. This port heavily relies on the 3DS's 3D GPU hardware to achieve 60 FPS (or close to 60 with frame skips). Since we are using the hardware, some games that utilise special palette effects may not work so well.
PicoDrive (Sega Master System / Mega Drive) core
This is a port of notaz's PicoDrive emulator to the old 3DS and old 2DS. Currently supports Sega Master System and Mega Drive games only. If you want Sega CD and 32X support, Retroarch is your best bet for now.