3DS:
Super Mario 3D Land
Mario Kart 7
The Legend of Zelda: Ocarina of Time 3D
The Legend of Zelda: Majora's Mask 3D
The Legend of Zelda: A Link Between Worlds
Pokemon X/Y
Fire Emblem Awakening
Kid Icarus: Uprising
Super Smash Bros. for Nintendo 3DS
Bravely Default
Since we're also talking about the New 3DS, don't forget about Xenoblade Chronicles.
"Just for comparison Uncharted 4 was 20x bigger than Splatoon 2. This shows the huge difference between Sony's first-party games and Nintendo's first-party games."