Does Kid Icarus: Uprising count as second party? I am quite confused about that. If not, I nominate Fire Emblem Awakening. I doubt Ganbarions Pandora's Tower falls under the second party umbrella (although Nintendo published), this is a game I like very much. Same with Another Code R from Cing, which was Nintendo published and now in a weird move got a remake as Nintendo first party.
So yeah, my difficulties are in the area of identifying what counts as second party.