This is a list of interesting-enough 3DS games, grouped by publisher and franchise. Updated Sep 2022, as there are no more 3DS games coming out.
Nintendo
- Animal Crossing New Leaf
- Boxboy - BoxBoy!, BoxBoxBoy!, Bye-Bye BoxBoy!
- Code Name: S.T.E.A.M.
- Dillon - Rolling Western, Last Ranger, Dead Heat Breakers
- Ever Oasis
- Fantasy Life
- Fire Emblem - Awakening, Fates, Echoes
- HarmoKnight (eShop)
- Kid Icarus Uprising
- Kirby - Triple Deluxe, Planet Robobot
- Mario - Super Mario 3D Land, New SMB 2, Mario and Donkey Kong: Minis, Luigi’s Mansion Dark Moon
- Mario RPGs - Superstar Saga remake, Dream Team, Sticker Star, Paper Jam
- Mario Sports - Tennis Open, Golf World Tour
- Metroid Samus Returns
- Picross - Picross 3D: Round 2, Pokemon Picross
- PilotWings Resort
- Pocket Card Jockey (eShop)
- Pokemon RPGs (I guess) - Ultra Sun Moon, XY, ORAS
- Pokemon spinoffs - Art Academy, Battle Trozei, Shuffle
- Professor Layton series
- Pushmo - Pushmo, Crashmo, Stretchmo
- Rhythm Heaven Megamix
- Star Fox 64 remake
- Tokyo Crash Mobs
- Zelda - A Link Between Worlds, OoT remake, MM remake
Square Enix
- 7th Dragon III Code: VFD
- Bravely Default & Bravely Second
- DQ7 remake & DQ8 remake
- Theatrhythm Final Fantasy & Curtain Call
Atlus
- Etrian Odyssey - 3, 4, 5, Untold, Untold 2, Mystery Dungeon, X
- Legend of Legacy & The Alliance Alive
- Radiant Historia: Perfect Chronology (remake)
- SMT Devil Summoner - Soul Hackers (remake/first English release),
- SMT Devil Survivor - Devil Survivor Overclocked, Devil Survivor 2,
- SMT Persona - Persona Q, Persona Q2
- Shin Megami Tensei - SMT4, SMT4 Apocalypse, Strange Journey Redux
Sega
- 3D remake series (Gunstar Heroes, Streets of Rage 2, etc)
- Rhythm Thief & the Emperor’s Treasure
- Stella Glow (see also Atlus, which is part of Sega)
Misc
- Capcom - Phoenix Wright: Ace Attorney Trilogy
- Inti Creates - Azure Striker Gunvolt 1 & 2
- Level-5 - Guild series (small games from notable designers) - Liberation Maiden, Aero Porter, Crimson Shroud, Weapon Shop de Omasse, Attack of the Friday Monsters, Bugs vs. Tanks, The Starship Damrey.
- NIS America - Culdcept Revolt
- Xseed Games - Story of Seasons (aka Harvest Moon)
good on 3DS but available/better on other systems:
- Kingdom Hearts 3D: Dream Drop Distance
- Maldita Castilla EX
- Mighty Gunvolt
- Shovel Knight
- Sonic Generations
- SteamWorld series - Dig, Dig 2, Heist
- VVVVVV
- Xenoblade Chronicles
- Rune Factory 4
- Zero Escape: Virtue’s Last Reward
also:
- lots of Monster Hunter games - eclipsed by MH World and MH Rise
- Pokemon I guess
- Super Smash Bros - eclipsed by SSBU