Good to see Puyo Puyo on there, though Puyo Puyo Tsuu is better. Amazed to see it above such staples as Monster Hunter and Wizardry, though. Also good to see Tactics Ogre in the list, though I wouldn't put it in the top ten, or even necessarily in the top one hundred games of all time. But then, I play non-Japanese games in addition to Japanese games, so a lot of my votes wouldn't even be in the top one thousand.
Also, a Kingdom Hearts game being above Chrono Trigger and in the top twenty is proof of Japanese gamers' idiocy, as is them placing the two most overrated Final Fantasy titles at the top of the list.
For comparison, there was a "top 200 games of all time" list in a recent Game Informer that put The Legend of Zelda in the top spot (the same happened in their "top 100 games of all time" list). And I believe World of WarCraft came in at number four. However, that list was chosen by the magazine's editors, not the readers. Not that a reader-chosen list really would've been any better, considering the magazine's demographic.
Also, the Famitsu list was done in 2006. Were they to do such a list this year, we'd probably see all ten of the top spots occupied by Final Fantasy and Dragon Quest games - in particular, I wouldn't be surprised at all to see Dragon Quest IX in the top spot or at least in second place.