I was never in much doubt about this. But to clear one item out of the way, I am disqualifying the top book by ownership which is tagged "Netherlands" on GoodReads because only a small section (though important for the story) is set in Amsterdam; it is mostly about teenagers suffering from cancer in Indianapolis. It was published in 2012 and the film adaptation came out last year. It is:
The Fault in Our Stars, by John Green
Excluding that, there is a very clear winner by ownership on both LT and GR, also tagged "Netherlands" most on GR and second-most on LT, a non-fiction memoir of living in Amsterdam in desperate and tragic circumstances, written in 1942-44 and published in 1947, two years after the author's death in Belsen. I suspect that she is the youngest writer who will feature in any of these posts, by quite a long way. I'm actually in the middle of reading it in the original Dutch at the moment. Needless to say, it is:
The Diary of a Young Girl / Het Achterhuis, by Anne Frank
One other book worth noting here is the one most often tagged "Netherlands" on LibraryThing, and with second most readers after the 1940s memoir. It's a novel set in Delft around the life of Vermeer, ie the seventeenth century, published in 1999 and adapted for film in 2003. It is:
Girl with a Pearl Earring, by Tracy Chevalier
The best-known work of fiction, as opposed to non-fiction, by a Dutch writer set in the Netherlands appears to be a 2009 novel about two brothers out for dinner with their wives, discovering that their sons have done something dreadful. Apparently Cate Blanchett is even now directing an English-language film version. It is:
Het Diner / The Dinner, by Herman Koch.