Golden Abyss really suffered from the touch screen controls.
The GCN version of Mega Man Anniversary, for some reason, has the shoot/jump buttons reversed, and you can't change them.
Throwing grenades in Rocket Birds on Vita touchscreen was a pain in the butt.
Most things that involved shaking, jerking, or rotating the Sixaxis, e.g., Killzone 2, Uncharted. It worked really well in games like Folklore though.