Sinobi shows the top 50 selling titles in 21st century in Japan. As expected, DS ruled Japan in last decade.
http://ameblo.jp/sinobi/entry-11658137027.html
Data from 2000/1/1 - 2013/9/29
01:NDS「New Super Mario Bros.」6,424,042
02:NDS「Pokemon Diamond/Pearl」5,826,538
03:NDS「Pokemon Black/White」5,488,538
04:GBA「Pokemon Ruby/Sapphire」5,337,045
05:NDS「Animal Crossing WW」5,239,465
06:NDS「Brain Training 2」5,082,322
07:Wii「New Super Mario Bros. Wii」4,567,937
08:PSP「Monster Hunter Portable 3rd」4,502,846
09:NDS「Dragon Quest IX」4,155,855
10:NDS「Mario Kart DS」4,002,914
11:NDS「Pokemon Heart Gold/Soul Silver」3,936,086
12:NDS「Brain Training」3,847,136
13:3DS「Animal Crossing NL」3,823,486
14:Wii「Wii Sports」3,724,264
15:NDS「Tomodachi Collection」3,690,500
16:Wii「Mario Kart Wii」3,674,565
17:Wii「Wii Fit」3,561,787
18:PS2「Dragon Quest VIII」3,555,459
19:Wii「Wii Sports Resort」3,143,214
20:GBA「Pokemon Fire Red/Leaf Green」3,076,047
21:NDS「Pokemon Black 2/White 2」2,997,712
22:Wii「Wii Play」2,804,201
23:NDS「Pokemon Platinum」2,604,510
24:3DS「Monster Hunter 4」2,542,114
25:PSP「Monster Hunter Portable 2nd G」2,453,132
26:Wii「Wii Fit Plus」2,409,957
27:Wii「Wii Party」2,382,177
28:PS2「Final Fantasy X」2,325,215
29:PS2「Final Fantasy XII」2,322,541
30:Wii「Smash Bros. Brawl」2,279,108
31:NDS「English Training」2,228,912
32:GBA「Pokemon Emerald」2,197,017
33:3DS「New Super Mario Bros. 2」2,114,108
34:NDS「Mario Party DS」2,112,218
35:3DS「Mario Kart 7」2,087,411
36:NDS「Nintendogs」2,080,644
37:PS2「Final Fantasy X-2」1,960,937
38:NDS「Rhythm Heaven Gold」1,917,454
39:PS3「Final Fantasy XIII」1,905,979
40:3DS「Super Mario 3D Land」1,881,831
41:PSP「Monster Hunter Portable 2nd」1,723,187
42:PS2「Dragon Quest V」1,614,806
43:3DS「Monster Hunter 3G」1,589,804
44:NDS「Big Brain Academy」1,589,539
45:NDS「Knowledge Training」1,569,882
46:NDS「Pokemon Mystery Dungeon: Explorers of Time and Explorers of Darkness」1,551,640
47:Wii「Mario Party 8」1,470,332
48:NDS「Dragon Quest Monster Joker」1,467,179
49:PS2「GT3 A-spec」1,438,743
50:3DS「Tomodachi Collection New Life」1,433,836