These one
Famitsu 3DS titles above 100k, not everyone has been updated to the most recent date for Famitsu ( two weeks ago )
[3DS] Mario Kart 7 (Nintendo) - 451.932 / 1.471.151 / 30,72% 01/12/11
[3DS] Super Mario 3D Land (Nintendo) - 344.698 / 1.341.040 / 25,70% 03/11/11
[3DS] Monster Hunter 3G (Capcom) - 471.055 / 1.128.359 / 41,75% 10/12/11
[3DS] The Legend of Zelda: Ocarina of Time 3D (Nintendo) - 182.998 / 515.284 / 35,51% 16/06/11
[3DS] Nintendogs+cats (Nintendo) - 68.973 / 471.911 / 14,62% 26/02/11
[3DS] Inazuma Eleven Go (Level 5) - 141.458 / 377.488 / 37,47% 15/12/11
[3DS] Professor Layton and the Mask of Miracles (Level 5) - 117.589 / 363.030 / 32,39% 26/02/11
[3DS] Pokemon Rumble Blast (Nintendo) - 91.613 / 278.990 / 32,84% 11/08/11
[3DS] One Piece: Unlimited Cruise SP (Bandai Namco) - 76.578 / 229.032 / 33,44% 26/05/11
[3DS] Resident Evil: Revelations (Capcom) - 160.575 / 160.575 / 100,00% 26/01/12
[3DS] Samurai Warriors: Chronicles (Koei Tecmo) - 43.044 / 150.080 / 28,68% 26/02/11
[3DS] Super Street Fighter IV 3D Edition (Capcom) - 38.557 / 137.883 / 27,96% 26/02/11
[3DS] Resident Evil: The Mercenaries 3D (Capcom) - 61.306 / 128.133 / 47,85% 02/06/11
[3DS] SD Gundam G Generation 3D (Bandai Namco) - 83.456 / 119.610 / 69,77% 22/12/11
[3DS] Tales of the Abyss (Bandai Namco) - 68.218 / 114.439 / 59,61% 30/06/11
[3DS] Ridge Racer 3D (Bandai Namco) - 34.663 / 110.415 / 31,39% 26/02/11
[3DS] Dragon Quest Heroes: Rocket Slime 3 (Square Enix) - 45.529 / 108.286 / 42,05% 02/11/11
[3DS] Winning Eleven 3DSoccer (Konami) - 26.222 / 107.274 / 24,44% 26/02/11
Just for curiosity.
You have listed all 3DS games that have sold over 100k units since the release of the 3DS (from 26/02/11 to 26/01/12 - 49 weeks).
Here there is a practically equivalent list (from 29/11/04 to 21/11/05 - 52 weeks) with all NDS games that end up selling over that mark too.
21/11/05 [NDS] Animal Crossing: Wild World (Nintendo) 335.425 / 5.134.724 6,53%
16/05/05 [NDS] Brain Training (Nintendo) 44.166 / 3.821.387 1,16%
18/04/05 [NDS] Nintendogs (Labrador, Dachshund, Chihuahua) (Nintendo) 135.674 / 1.944.674 6,98%
27/06/05 [NDS] Big Brain Academy (Nintendo) 52.525 / 1.585.330 3,31%
29/11/04 [NDS] Super Mario 64 DS (Nintendo) 120.062 / 1.162.478 10,33%
29/11/04 [NDS] WarioWare: Touched! (Nintendo) 117.677 / 1.136.255 10,36%
12/09/05 [NDS] Tamagotchi Connection: Corner Shop (Bandai) 107.499 / 1.110.046 9,68%
14/11/05 [NDS] Pokemon Mystery Dungeon: Blue Rescue Team (Pokemon Co.) 134.776 / 761.617 17,70%
31/10/05 [NDS] Clubhouse Games (Nintendo) 64.994 / 630.777 10,30%
08/08/05 [NDS] Jump! Super Stars (Nintendo) 202.139 / 549.265 36,80%
29/11/04 [NDS] Pokemon Dash (Pokemon Co.) 50.011 / 348.376 14,36%
21/03/05 [NDS] Kirby Canvas Curse (Nintendo) 72.102 / 315.211 22,87%
17/10/05 [NDS] Pokemon Puzzle (Pokemon Co.) 46.910 / 293.807 15,97%
18/04/05 [NDS] Naruto Shippuden: Saikyou Ninja Daikesshuu 3 (Tomy) 66.897 / 220.928 30,28%
24/01/05 [NDS] Yoshi Touch & Go (Nintendo) 52.407 / 197.337 26,56%
17/10/05 [NDS] Super Princess Peach (Nintendo) 29.164 / 196.641 14,83%
29/11/04 [NDS] Daigasso! Band Brothers (Nintendo) 32.272 / 164.166 19,66%
11/07/05 [NDS] Naruto RPG 2: Chidori Vs. Rasengan (Tomy) 31.451 / 131.748 23,87%
12/09/05 [NDS] Phoenix Wright: Ace Attorney (Capcom) 50.469 / 117.784 42,85%
14/03/05 [NDS] Harvest Moon: Colobocle Station (Marvelous Entertainment) 22.026 / 107.136 20,56%
18/07/05 [NDS] Mega Man Battle Network 5: Double Team (Capcom) 17.317 / 106.526 16,26%
21/02/05 [NDS] Another Code (Nintendo) 48.357 / 105.452 45,86%
18/07/05 [NDS] Yu-Gi-Oh! Duel Monsters: Nightmare Troubadour (Konami) 39.016 / 102.249 38,16%
29/11/04 [NDS] Feel the Magic: XY/XX (Sega) 27.062 / 100.263 26,99%
Some notes:
The LTD sales are updated to March 2010 (thanks Chris 1964 for sharing your database with us), so it is likely that some 3DS games will end up selling over 100k units when all is said and done. Examples: Pilotwings Resort, Starfox 64 3D or Rhythm Thief & the Emperor's Treasure.
New Love + and Theatrhythm Final Fantasy that were released a day ago are likely to sell over 100k units, so since I counted the 52 first weeks for the NDS titles these two games will have to be take into account too.