This is a list based in three different japanese popularity polls of "Top 100 Games of All Time".

One of them is a pretty famous one done by Famitsu back in 2006 (https://vgsales.fandom.com/wiki/Famitsu_Japan%27s_100_favorite_video_games)
Another one was done by Famitsu again in 2017 (https://nintendoeverything.com/famitsu-readers-choose-the-top-100-best-games-of-all-time/)
And the last one was by TV Asahi (which apparently is a very famous channel in Japan) in 2021. I guess is fair to say that this one was voted by a more casual audience (https://kotaku.com/poll-here-are-japans-top-100-video-games-of-all-time-1848275437)

What I did was create a single list based on the average ranking of those games in each list.
The reason there's only 64 entries is because I've only counted the games that appeared in more than one list.
For the ones that appeared in only two of the three lists, I gave the score equivalent as if the game was placed 101 in the missing one.
As for ties, I just pick the game that ranked higher in the most recent one.
By the way, the top 2 games were tied in score, the reason I put FFVII is because of what I've mentioned above. I swear I'm not a FFVII fanboy, I just had to choose a criteria for tiebreak.

Since all of us (I guess?) see games through a western perspective, I think is pretty cool to see the games that people from Japan like the most, since it's a whole different world there, and at the same time it's such a important place for the gaming world, both in influence and market.

Also, I'm using remake entries for the first Dragon Quest games because I refuse to see that stupid cover and I don't have the option of using the actual original game because Backloggd sucks.

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Franchises that appeared multiple times:

Final Fantasy (11)
Dragon Quest (8)
The Legend of Zelda (4)
Persona (3)
Super Mario (3) + Super Mario Kart
Sakura Wars (3)
Animal Crossing (2)
Kingdom Hearts (2)
Kirby (2)
Metal Gear (2)
Mother (2)
Xeno (2)