Citra

Citra is a Nintendo 3DS emulator for PC that can run commercial games at 100% of their speed. Plus it can improve the games' graphics way past their humble Nintendo resolution.

The emulator can display both screens at the same time, though if you prefer you can set it to one screen at a time by assigning a button to alternate between screens. As far as the controls, you can use the keyboard or map the controls to an external gamepad. You can also use the touchscreen controls by setting the cursor directly on the point where you want to click.

Citra can run a wide range of games from the Nintendo 2D and 3D catalog, though it's in the 3D games where it really shines. It completely transforms the resolution of the games to the point that you wouldn't even guess they come from a handheld console. Games such as Pokemon Sun and Moon or The Legend of Zelda: A Link Between Worlds look truly impressive.

Citra is quite possibly the best and most advanced Nintendo 3DS emulator out there. An open-source volunteer project that lets you play your handheld games on desktop machines.