The Legend of Zelda: Ocarina of Time 3D is a good one. Everything's been remastered, graphically and several gameplay tweaks have made it that much more fun to play. Although playing the ocarina sucks for me because of the way they changed up which buttons play which notes.
Theatrythmn Final Fantasy is an awesome action rhythm game that, so far, has gotten many many hours out of me. It's addicting as all get out.
Many people would recommend Fire Emblem: Awakening. I can't get into SRPGs, personally, so I haven't bothered with it.
Definitely get Tales of the Abyss if you're into JRPGs. It's an exact port of the PS2 version, but damn is it still great.
If you're into older games, I'd definitely recommend going onto the Nintendo eShop and checking out their Virtual Console library. Megaman 1-5, Metroid II, The Legend of Zelda: Link's Awakening DX/Oracle of Ages/Seasons, Mario Picross. They even made a Zelda: Four Swords Anniversary, which is exactly the same as Four Swords, but can be played alone.
All kinds of amazing games, not including their eShop only titles that aren't VC, like SpeedX 3D Hyper Edition and Zenonia. All great games.
Not to mention the entire DS library at your disposal:
Phoenix Wright Ace Attorney
Phoenix Wright Ace Attorney: Justice for All
Phoenix Wright Ace Attorney: Trials and Tribulations
Apollo Justice Ace Attorney
Miles Edgeworth Ace Attorney: Investigations
Phoenix Wright Ace Attorney: Dual Destinies(this title is actually 3DS and not yet released)
Hotel Dusk: Room 215
9 Hours, 9 Persons, 9 Doors
Megaman Zero Collection
So many more. Definitely do not neglect to check out the DS library as well.