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There is a lot:
1. Resident Evil 4
2. Chrono Trigger
3. Final Fantasy VI
4. Viewtiful Joe
5. Resident Evil (GC)
For second-party games/games developed by another company, but published by Nintendo, there are classics like Goldeneye, Perfect Dark, Donkey Kong Country Series, both Banjo-Kazooie Games, Eternal Darkness, and Super Mario RPG.
Honorable Mentions include: Street Fighter 2, Megaman 2, Megaman X, Super Castlevania IV, Final Fantasy IV.