The first game that springs to mind for me is the Donkey Kong game that came out early in the original 3DS's lifecycle which I found unplayable due to it's choppy framerate - anyone tested? would it possibly run at 60fps like the Wii counterpart?
Baffles me that Nintendo didn't patch pokemon themselves to take advantage of the new CPU, this was the first thing everyone insinuated they would do when the N3DS was announced and here's proof that it would (does!) work.