Verified answer

Kinokuniya : largest book store chain in Japan and also Asia

Book off : largest used book store chain in Japan and also the world

Melon Books : most famous Doujin books store

Animate or Gamers : most famous manga book store

Junkudo Ikebukuro shop : widest book store in japan

Village Vanguard : famous subculture / underground book store.

Kanda Jinbo cho : largest book town in the world. there are many small classic used book stores.

According to Wikipedia, Kinokuniya, Junkudo and Maruzen are top 3 in sales.

But about the popularity, I think the most is Villrdge Vanguard.

http://www.village-v.co.jp/

And Keibunsha Ichijoji branch in Kyoto and Shinaishoten in Tokyo are famous for it's fan.

http://www.keibunsha-books.com/

http://kouenjishorin.jugem.jp/?cid=2

The most popular are:

Jiyushobou

Sanyoudou

Maruzen

Kinokuniya

Book Off

Kinokuniya

"Book Off" is another popular place. Here you can find used books, cd's, video games, dvds etc.

Kinokuniya

Sanseido

Don't forget Junkudou.