Super Mario 3D Land
Luigi's Mansion: Dark Moon
Legend of Zelda: A Link Between Worlds
Animal Crossing: New Leaf
Monster Hunter Generations
Rune Factory 4
Dragon Quest VIII
Xenoblade Chronicles 3D
Pok?mon Sun/Moon
Shin Megami Tensei IV, and Apocalypse
Zero Escape: 999(DS), Virtue's Last Reward, and Zero Time Dilemma
ANY pokemon!
the latest final fantasy (a must)
LoZ Ocarina of Time! or any LoZ game tbf
animal crossing (of course)
may seem like a child for this one, but nintendogs and cats!! it is a great game to play chill
either mario party is a great game to have as well, its just a good game to play with people!
Super Mario 3D Land
Mario Kart 7
Luigi's Mansion: Dark Moon
Animal Crossing: New Leaf
Fire Emblem: Awakening
Super Smash Bros. for the Nintendo 3DS
Rhythm Heaven Megamix
Legend of Zelda: Ocarina of Time 3D
Legend of Zelda: Majora's Mask 3D
Star Fox 64 3D
All the above suggestions are good I really enjoyed Ace Attorney: Dual Destinies to but I guess that's a more catered
Best E-shop game would be Attack of the Friday Monsters. It's a really amazing visual novel type game set in Japan, it's really charming. And X and Y are probably the best Pokemon games for this console imo.
Rune factory 4
Acnl (But you probably already have that since you're here LOL)
Mariokart 7
Luigi's mansion dark moon
Monster hunter 4 ultimate
Bravely Default / Bravely Second
Legend of Zelda OOT, ALBW and MM
Kid Icarus Uprising
Smash Bros 3DS
Hyrule Warriors
Pokemon in general (X/Y is really nice tho)
Kingdom Hearts Dream Drop Distance
If you're a Disney fan, Disney art academy is actually really fun. I got it more for the sharing of drawings rather than the lessons, but it's all really enjoyable. Check out the Miiverse too, there are AMAZING drawings there. I'd definitely recommend picking it up if you're into making art on the 3ds. It's only 20 dollars at Gamestop too.
The top game I would recommend is Monster Hunter X, it is the expansion of Monster Hunter generations and has tons more content and some new monsters (over 70 new hunts to take, not including DLC).
There are new abilities as well and more customization options, as well as new palico types and new hunter arts and skills.
+ The soundtrack is amazing.
Next up would be animal crossing welcome amiibo, for the obvious reasons ?ω?
Ultra Sun/Moon is coming out soon, so that's the game to buy if your into competitive pokemon, but if your going for a full on experience buy Omega Ruby or Alpha Sapphire, both games have allot more content than sun/moon and x/y. + if you want to run a legit Hidden Ability egg service this is the game to buy, since most hidden ability pokemon are obtained on this game.
I know I posted on here earlier, but Scribblenauts is pretty fun too. The Wii U version is much better though, but if you only have a 3ds, I'd highly reccomend picking it up. It's pretty cheap too. It's worth the like, 5 dollars.