Sky3DS+ => the best choice for Nintendo 3DS when it comes to 3DS game compatibility. But it can´t handle any other formats like nds or gba, emulators or any retro games. If you like to play only NDS games on your Nintendo 3DS you may use most of NDS flash carts.
SuperCard DS Two Plus => this is the best choice for Nintendo NDS Lite or Nintendo 3DS, for retro, emulators, multimedia fies, nds games and 3DS games with some lower compatibility than Sky3DS+. It have very advanced hardware, better than any other flash carts, it's fast.
EZ Flash 4 => is the best choice for those who have the GBA. It works on the fat NDS in Slot-2 as well.