Over at SFWA, Nick Mamatas and Masumi Washington list, and comment on, the list of all-time best Japanese SF, as voted on by readers of Japan’s SF Magazine in 2006.
1. Hyakuoku no hiru to senoku no yoru
(Ten Billion Days and One Hundred Billion Nights) by Ryu Mitsuse (1967)
An epic, cosmic adventure in the manner of Arthur C. Clarke, covering the evolution of humanity, the lives of Plato, Christ, and the Buddha, a future technodystopia, and the very heat death of the universe itself. For pure “sensawunda,” it gets no better. Haikasoru will be releasing this book in its first English translation in November 2011. Longtime US SF readers may remember Ryu Mitsuse’s “The Sunset, 2217 A.D.,” which appeared in Frederik Pohl’s Best Science Fiction for 1972.
2. Hateshinaki nagare no hate ni
(At the End of the Endless Stream) by Sakyo Komatsu (1966)
Thematically similar to Mitsuse’s epic, Komatsu’s story involves a young physicist shown an hourglass, the sand of which never stops flowing. Even stranger, the glass was discovered buried in a stratum associated with the Upper Cretaceous. The hourglass is key to a billion-year war in which humans are pawns…and then humans begin to vanish. Sakyo Komatsu was one of the grandmasters of Japanese SF—three of his books appear in this top ten list—sadly, he passed away in July 2011, at the age of eighty. – continue reading!
The World SF Blog 
Are these translated in english anywhere?
Several are. Haikasoru is publishing TEN BILLION DAYS AND ONE HUNDRED BILLION NIGHTS in November. We also published YUKIKAZE in English, and its sequel. JAPAN SINKS isn’t currently in print in English, but there have been a few editions over the years and it occasionally shows up in used bookstores.
Thanks for posting this! I’ve been meaning to catch up with my Japanese sci fi literature and can really use some suggested titles.