Captain Toad - It's a short puzzle game. One I enjoyed a lot. The Captain Toad amiibo adds a new mode to the game. Apart from the last stage in this game, it's great. I liked it so much. Not everyone's taste though but it's wroth lookingt into.
Art Academy Atleir/Home Studio - If you want to learn how to draw it's great. I suck at it but learning to draw with the lessons here is really fun. The only downside is there is no music during the draw segments. The lessons are very good though as is the free draw canvas.
Affordable Space Adventures - One of the most unique uses of the gamepad. Digital only but it's really just that good. You have to move the ship to the end of the stage but you don't just move it. You have to deal with power levels, lights, type of thrust, it's in my opinion as much a puzzle game of working out what to do as it is an action style game.
NintendoLand - get it cheap on Ebay for like $20 and you'll have a ball with it, even if you don't have a wiimote, you can use the gamepad for about half the game's content. Not worth full price, but at $20 it's a great little collection of games. Some of them are very hard though.
Yooka-Laylee - The amazing looking platformer from Playtonic (the best of the old Rare). It's the spiritual sucessor of Banjo-Kazooie. I am sure it'll be on the eShop when it releases. If you like 3D collectathons like SM64, Banjo-Kazooie, DK64, etc etc, then you'll love Yooka-Laylee.