Brain Training 2 passes FF XII for 2006, not to mention the 450k sold in 2005!
http://www.everythingandnothing.org.uk/vg/japyearly.php?year=2006
1 Brain Training 2 DS Nintendo 2,276,500 2,735,000
2 Final Fantasy XII PS2 Square 2,275,500 2,275,500
3 Animal Crossing: Wild World DS Nintendo 1,590,750 3,060,750
4 New Super Mario Bros DS Nintendo 1,546,000 1,546,000
5 Brain Training DS Nintendo 1,304,750 2,584,250
6 English Training DS Nintendo 1,184,500 1,184,500
7 World Soccer Winning Eleven 10 PS2 Konami 816,750 816,750
8 Tetris DS DS Nintendo 668,750 668,750
9 Mario Kart DS DS Nintendo 638,750 1,512,750
10 Pokemon Rangers DS Nintendo 592,750 592,750
11 Samaurai Warriors 2 PS2 Koei 556,750 556,750
12 Monster Hunter 2 PS2 Capcom 555,500 555,500
13 Dirge of Cerberus: Final Fantasy VII PS2 Square 492,250 492,250
14 Monster Hunter Portable PSP Capcom 375,750 664,250
15 Mother 3 GBA Nintendo 368,750 368,750
16 Shin Onimusha: Dawn of Dreams PS2 Capcom 333,250 333,250
17 Brain Flex DS Nintendo 316,500 1,262,250
18 Mario + Luigi 2: Partners In Time DS Nintendo 293,750 440,000
19 Tamogotchi Connection: Corner Shop! DS Bandai 284,750 1,103,500
20 Nintendogs DS Nintendo 274,500 1,321,500
21 Seiken Densetsu DS: Children Of Mana DS Square 271,750 271,750
22 Dragon Quest Yangus PS2 Enix 269,500 269,500
23 Gundam Clamix U.C. PS2 Bandai 231,250 231,250
24 Daredemo Asobi Taizen DS Nintendo 228,000 596,250
25 Lets Make a J-League Pro Soccer Club European Cham PS2 Sega 218,250 218,250
26 Kingdom Hearts II PS2 Square 201,750 1,161,500
27 Ace Combat Zero PS2 Namco 190,750 190,750
28 Powerful Pro Major League PS2 Konami 188,000 188,000
29 Super Mario Strikers GC Nintendo 185,250 185,250
30 Suikoden V PS2 Konami 182,500 182,500