Only including 3DS games. Not apps.

1.) Monster Hunter 3 Ultimate - 255:05 (add another 100 hours including Wii U ver)
2.) Pokemon Y - 175:07
3.) Fire Emblem Awakening - 133:17
4.) Bravely Default - 79:34
5.) Monster Hunter 4 Ultimate - 76:37
6.) Shin Megami Tensei: Devil Survivor Overclocked - 48:40
7.) Shin Megami Tensei IV - 34:05
8.) Pokemon Omega Ruby - 28:46
9.)Shin Megami Tensei: Devil Survivor 2 Record Breaker - 25:44 (not yet completed, currently playing)
10.) Codename S.T.E.A.M - 16:24

Wait, 3ds tracks ds game times as well?

That is correct. It basically tracks anything you do on the 3DS

Previous:

1. Animal Crossing: New Leaf (105:49)
2. Smash Bros. (48:46)
3. Theatrhythm: Final Fantasy (39:13)
4. Ocarina of Time 3D (29:22)
5. Final Fantasy IV (27:37)
6. Streetpass Mii Plaza (27:17)
7. New Super Mario Bros. 2 (21:51)
8. Super Mario 3D Land (21:26)
9. Mario Kart DS (20:27)
10. Mario Kart 7 (17:42)

Now:
1. Animal Crossing: New Leaf (105:49)
2. Smash Bros. (52:06)
3. Theatrhythm: Final Fantasy (39:13)
4. Ocarina of Time 3D (29:22)
5. Final Fantasy IV (28:43)
6. Streetpass Mii Plaza (27:29)
7. New Super Mario Bros. 2 (21:51)
8. Super Mario 3D Land (21:26)
9. Mario Kart DS (20:27)
10. Mario & Luigi: Bowser's Inside Story (20:24)

Basically, not a lot of change. Besides the few that changed up there, the only 3DS games I really played over the summer were Shovel Knight and Steamworld Dig.

1.) Pokemon Y - 150:04
2.) Monster Hunter 4 Ultimate - 120:24
3.) Kingdom Hearts 3D: Dream Drop Distance - 117:27
4.) Pokemon Omega Ruby - 93:02
5.) Bravely Default - 81:49
6.) The Legend of Zelda: A Link Between Worlds - 80:56
7.) The Legend of Zelda: Ocarina of Time 3D - 76:39
[Nintendo eShop] - 63:39
[StreetPass Mii Plaza] - 58:26
8.) Resident Evil: The Mercenaries 3D - 52:40
9.) Monster Hunter 3 Ultimate - 50:22
[Internet Browser] - 47:12
10.) The Legend of Zelda: Spirit Tracks - 45:40

I was surprised to see that The Legend of Zelda: Majora's Mask 3D did not make it onto the list, however, I am sure that it will as I am planning on having a second playthrough before year's end.
I am surprised by how much I played Resident Evil: The Mercenaries 3D.
I am sure that more DS titles would have made it on this list had we accounted for my playtime on the DS as well.

I've gone through 3 3DS's at this point (and I've never transferred any data, since I don't own any digital games) so honestly I have no clue at all.

Finally getting around to doing this! My times aren't very impressive, but oh well.

1. Animal Crossing: New Leaf (91:42)
2. Mario & Luigi: Dream Team (47:47)
3. Bravely Default (39:54)
4. The Legend of Zelda: Majora's Mask 3D (39:33)
5. The Legend of Zelda: Ocarina of Time 3D (35:17)
6. Tomodachi Life (29:17)
7. Kirby: Triple Deluxe (28:56)
8. Professor Layton vs Phoenix Wright: Ace Attorney (28:33)
9. Pokemon Alpha Sapphire (27:08)
10. Pokemon Y (26:14)

Xenoblade Chronicles 3D should move up the ranks soon, since I've gotten back into it. The Legend of Legacy and Zelda Tri Force Heroes may make the list sometime this year. Don't see New Leaf ever moving from the top spot though.

They are the perfect games if you go by bus. Also Shuffle gets constantly updates (new pokémon) and is kept fresh this way.

1: Pokemon X (475:21)
2: Fire Emblem: Fates (205:12) (this was the first Fire Emblem Game I bought and I love love love it, all three routes!)
3: Pokemon Alpha Sapphire (185:37)
4. Pokemon Black 2 (158:25)
5. Super Mario 3D Land (100:07)
6. Luigi's Mansion 2 (98:05)
7. Fire Emblem: Awakening (96:29)
8. Mario Kart 7 (94:11)
9. The Urbz: Sims in the City (85:31) (I really cannot explain why I like this game so much)
10. Pokemon SoulSilver (83:13)

I only bought Awakening after clearing both Hoshido and Nohr in Fates, so that's why it's so much lower.

Wow. I need to get my 3DS back.

Anyway...I've played ~1600 hours on my 3DS since March 2014, which is when I bought it.

FE Awakening is on top with 210+ hours, second play through.
SMT DS2: Record Breaker is second with 140+ hours, third play through.
Bravely Default is at ~100 hours or so. Finished once, and used to bring additional Miis into the Mii Plaza.
EO Untold is at ~85 hours, second play through.
Persona Q is at ~80 hours, practically finished though I haven't beaten the final boss yet.
Conception II is at ~80 hours, too, got tired and left the final labyrinth unfinished. I should finish it for Serina.
SMT IV is at ~70 hours. Felt too short and easy, finished once.
SMT DS: Overclocked at ~65 hours, finished once (no 8th day).
Mario & Luigi: Dream Team at ~65 hours, got bored and accidentally wiped my file once. Now I'm enjoying it!
EO IV is at ~60 hours, finished once, but not 100%. Felt short.