Info courtesy of YSO and various IR reports.  Sorted by publisher, titles in english where applicable.

Nintendo

1. New Super Mario Bros. (DS) 5,660,000
2. Animal Crossing: Wild World (DS) 5,080,000
3. Brain-Age 2: More Training in Minutes a Day (DS) 5,030,000
4. Brain-Age: Train You Brain in Minutes a Day (DS) 3,920,000
5. Wii Sports (Wii) 3,640,000
6. Wii Fit (Wii) 3,610,000
7. Mario Kart DS (DS) 3,510,000
8. Wii Play (Wii) 2,800,000
9. Mario Kart Wii (Wii) 2,460,000
10. English Training: Have Fun Improving Your Skills (DS) 2,310,000
11. New Super Mario Bros. Wii (Wii) 2,000,000
12. Nintendogs (DS) 1,980,000
13. Mario Party DS (DS) 1,930,000
14. Friend Connection (DS) 1,880,000
15. Super Smash Bros. Brawl (Wii) 1,860,000
16. Rhythm Heaven (DS) 1,800,000
17. Imasara Hito ni wa Kikenai Otona no Joushikiryoku Training DS (DS) 1,660,000
18. Big Brain Academy (DS) 1,620,000
19. Wii Sports Resort (Wii) 1,410,000
20. Mario Party 8 (Wii) 1,390,000
21. Tetris DS (DS) 1,370,000
22. Wario Ware Touched! (DS) 1,240,000 
23. Animal Crossing: City Folk (Wii) 1,220,000
24. Super Mario 64 DS (DS) 1,190,000
25. Kirby: Squeak Squad (DS) 1,140,000
26. Kirby Super Star Ultra (DS) 1,118,000
27. Yoshi's Island DS (DS) 1,080,000
28. Wii Fit Plus (Wii) 1,070,000
29. Super Mario Galaxy (Wii) 1,000,000

Square Enix

1. Dragon Quest IX: Sentinels of the Starry Skies (DS) 4,150,000
2. Final Fantasy XIII (PS3) 1,800,000
3. Dragon Quest Monsters JOKER (DS) 1,500,000
4. Dragon Quest IV: Chapters of the Chosen (DS) 1,220,000
5. Dragon Quest V: Hand of the Heavenly Bride (DS) 1,200,000
6. Final Fantasy III (DS) 1,000,000

The Pokemon Company

1. Pokemon Diamond / Pearl (DS) 5,770,000
2. Pokemon Heart Gold / Soul Silver (DS) 3,130,000
3. Pokemon Platinum (DS) 2,480,000
4. Pokemon Mystery Dungeon: Explorers of Darkness / Time (DS) 1,580,000

Capcom

1. Monster Hunter Freedom Unite (PSP) 2,460,000
2. Monster Hunter Freedom 2 (PSP) 1,730,000
3. Monster Hunter Freedom Unite THE BEST (PSP) 1,100,000
4. Monster Hunter TRI (Wii) 1,100,000

SEGA

1. Oshare Majo Love & Berry: DS Collection (DS) 1,110,000

Bandai Namco

1. Tamagotchi Connection: Corner Shop (DS) 1,030,000

Level-5

1. Inazuma Eleven 2: Kyoui no Shinryokusha: Blizzard / Fire (DS) 1,000,000

Platform counts

• Nintendo DS: 30
• Wii: 12
• PSP: 3
• PlayStation 3: 1

Year counts

• 2004: 2
• 2005: 7
• 2006: 11
• 2007: 8
• 2008: 9
• 2009: 9

Genre counts

• RPG: 15
• Action: 7
• Simulation: 6
• Education: 5
• Minigames: 4
• Sports: 2
• Racing: 2
• Fitness: 2
• Music: 1
• Fighting: 1
• Puzzle: 1

even with all the ups and downs, it has been a great year for gaming in japan.

Holy crap @ the DS, insane~
What a gen for handhelds in Japan

Also yay for the Wii and FFXIII

More like a generation for DS and Nintendo games haha. But I think it is going back to what we are seeing around the world that Wii, PS3, and 360 have been great and big consoles but they are all completely overshadowed by the dominance of the Nintendo DS around the world and especially as we are seeing in Japan. Japan for this generation is definitely all about the DS games and the big Nintendo software that backed the DS system and the Wii system. Though it is nice to see a few other developers having some big games release as well.

i dunno if you should count the best monster hunter seperate from the original release, it's the same game.

Nintendo O_O

I think it's friend collection, but other than that good job.

Edit: I think you meant Pokemon Platinum instead of Emerald.

Oh yeah, I meant Platinum.

Tomodatchi Collection's likely localized name is Friend Connection btw, at least that's the title Nintendo's trademarked here.

It's how YSO and Capcom both count it.   Generally Japanese companies count budget reprints separately.  HMFU is notable as it's the first reprint to ever sell a million.

ok but it's the exact same game, and you're listing it twice.  As far as we're concerned on vgchartz it shouldn't be listed seperately.