Harmoknight is a real fun and cute rhythm game by Game Freak. Probably my favourite 3DS game.
Also The World Ends With You is a DS game but imo playing it on a DS or 3DS is the way to go rather than the newer ports without the absolutely buck wild control scheme so if that one passed you by and you like RPGs and weird control schemes then I would suggest that.
Seconding Picross 3D: Round 2. There's a ton of the best JRPGs of all time, like Bravely Default, Etrian Odyssey IV, and Shin Megami Tensei IV and SMTIV Apocalypse. Pocket Card Jockey is a masterpiece.
A Link Between Worlds is my favorite Zelda, the surprising open endedness is really refreshing. And Samus Returns debuts a lot of things people loved about Metroid Dread and is a great game on its own.
Rythem Heaven Megamix and Wario Ware Gold are compilation games for great series, but something is kind of lost taking them out of their original games. Megamix is maybe the one that's the most special in bringing everything together.
Rusty's Real Deal Baseball is completely nuts but I'm not sure if the experience is the same on a homebrew, as part of the game is haggling down the price of the DLC. Really good tho.
i think my favorite game on the 3ds in terms of hours i played it is still Fire Emblem Awakening, i didn't much care for Fates though plus it was kind of weirdly horny. Monster Hunter 4 was good too if you like those kind of grindy games.
twovests wrote
A Link Between Worlds
Super Mario 3D World
OoT 3D and MM 3D. (Both, IMO, the best way to play these games.)
Smash Bros 4 3DS (but it isn't anything too special if you already have Switch U)
Animal Crossing: New Leaf (might not be worth the time sink if you already have Wild World or New Horizons)
Mario Kart 7 is nice if you have friends who can play it too
And Mario & Luigi game
Cave Story 3D was pretty good
Star Fox 64 3D
New Super Mario Bros 2
I think there was also a Pokemon game on the 3DS
Various indie games like Steamworld Dig or Shovel Knight