Using the Activity Log, I personally did a top 25:
1. Super Smash Bros. - 979:02
2. Mario Golf: World Tour - 656:14
3. Animal Crossing: New Leaf - 602:51
4. Pokémon X - 550:09
5. Fire Emblem: Awakening - 528:46
6. Mario & Luigi: Dream Team - 458:40
7. Bravely Default - 341:18
8. Fantasy Life - 286:16
9. Mario Kart 7 - 279:07
10. Phoenix Wright: Ace Attorney - Dual Destinies - 249:47
11. Tales of the Abyss - 196:07
12. Xenoblade Chronicles 3D - 152:21
13. Dillon's Rolling Western - 102:59
14. Luigi's Mansion: Dark Moon - 93:06
15. Inazuma Eleven 3: Team Ogre Attacks! - 90:24
16. Professor Layton vs Phoenix Wright: Ace Attorney - 75:28
17. Inazuma Eleven GO: Light - 73:14
18. The Legend of Zelda: A Link Between Worlds - 67:53
19. Mario Party DS - 67:40
20. The World Ends With You - 49:54
21. Pullblox - 47:21
22. Donkey Kong Country Returns - 43:46
23. Pokémon Link: Battle! - 42:37
24. The Legend of Zelda (Virtual Console) - 38:31
25. Kirby: Triple Deluxe - 36:42
Omitted things like the friend list and internet browser because I wanted to include only games.