The PS2 may be flooding the list, but Nintendo is hanging in there!
Though Famitsu doesn't include every single retailer in Japan, their sales rankings are usually quite accurate. Below is the latest list for the top 30 (Japanese names). For games with two numbers, the first is the sales for the week, followed by overall sales.
2. Super Robot Wars A (GBA) 161272
7. Luigi Mansion (GC) 23457 : 140241
13. Wario Land Advance (GBA) 14209 : 193569
18. Mario Kart Advance (GBA) 8427 : 578209
19. Golden Sun (GBA) 6564 : 295807
20. Wave Race Blue Storm (GC) 6146 : 33897
23. Super Monkey Ball (GC) 5439 : 22194
25. Midaratto Nabe (Kabuto / Kuwagata) (GBA) 5238 : 39614
30. Super Mario Advance (GBA) 4354 : 702311
As you can see, GameCube isn't at the top, but all three games made it to the list! Also of note is that Mario Advance is still selling. Thanks goes to "HHH" for the sending the rankings to us!