Resident Evil Revelations, Best Resident Evil game in my opinion.
Fire Emblem Awakening, probably my favorite game on the 3DS, if you like turn based tactics games you need this game.
Mario Kart 7, really fun and a lot better than the Wii Mario Kart.
Super Mario 3D land, it's a Mario game they are all pretty good.
Kingdom Hearts 3D Dream Drop Distance, pretty fun and if you haven't played the other games in the series don't worry, they give you a readable summary of all the other games when they come up.
Kid Icarus Uprising, fun game, but you'll only be able to play it in small intervals as it kills your hand.
Professor Layton and the Miracle Mask, This is an assumption as I haven't played it but all the other Professor Layton games are amazing. Also if you haven't played any of the other Professor Laytons on DS get those as well they are amazing.
Zero Escape: Virtue's Last Reward, pretty good puzzle game with a branching story line. Also get 9 Hours 9 Persons 9 Doors for the DS if you haven't as Virtues Last Reward is the sequel to it.
Oregon Trail, because everyone needs Oregon Trail.
Star Fox 64 3D and Legend of Zelda Ocarina of Time 3D, if you haven't played either of these before you should get them, they are both solid games.