I suposse that games that heavily relies on Touchscreen. Ninja Gaiden Dragon Sword (DS), comes at my mind. For me, it wasn't a pleasant experience to play it on emu (i wanted to try it because you can upscale the game, but i don't feel confortable playing it with the mouse or the cellphone touchscreen). On real console its a blast. Ni no Kuni: Shikoku no Madoushi (relies on making magical simbols with the stylus) and Dragon Ball Origins 1 are another example. On 3DS, Dragon Ball Heroes Ultimate Mission X. The game is awesome but it loose some magic on emu (the double screen imitates the real arcade), plus it has a lot of quick time events that require movement with the stylus (like spining like a will, make a Z form, etc)