Forget the published lists; forget trying to rank books from both ends of the century (or millenium) on one list. Let’s stick with a reasonably modest period of time - the 1990s - and let’s have ‘best books’ recommendations from people who love to read, and have found a book or three that seem to stand out above all the other new books they’ve read, this decade.
Feel free to use genres - that is, feel free to say, ‘I thought _____ was one of the best [mystery/sf/fantasy/gothic/whatever]s of the decade’ to get it in here.
I’m going to kick it off with my favorite nonfiction book of the decade, and, IMO, one of the best of all time: The Song of the Dodo by David Quammen.
Not too many nonfiction books are page-turners, but this is one of them. I’m re-reading it for about the fifth time since it came out (in 1996) - I was inspired to pick it up again by the creation/evolution threads I’ve been posting on - and I can’t put it down. It’s that good.
So what’s it about? It’s about evolution and extinction, especially the latter - viewed from the POV of the origins and growth of an obscure field called island biogeography, which Quammen (quite successfully, IMO) argues is the key field for understanding both origins and ends. As he points out, Darwin was an island biogeographer even before he was a Darwinist. But it’s by following the arc of this field’s development that he manages to write a major book about extinction without getting into a gloomfest. And it works!
In a story that takes us from Darwin and Wallace through MacArthur and Wilson to the present, he takes us through many wonderful digressions that turn out to be essential to where he’d going - Komodo dragons, tree-climbing kangaroos, carnivorous parrots, the dodo (of course) and other exotica come up in the tale, because islands are where the oddities naturally develop - he feeds us little bits of the picture of how evolution and ecosystems - and ultimately extinction - work.
I use it as a reference (it’s wonderfully well-researched; the bibliography goes on for 24 pages of fine print), but first and foremost, it’s a really good read - jump in anywhere, read a few pages, and you’ll be swept along. There aren’t too many books for which that’s true, and it almost never happens in nonfiction. The Song of the Dodo is a spectacular exception.

I will add, though, that, IMO, Quammen’s The Song of the Dodo (see the OP) is another book where the book is far better than the (very complimentary) blurbs.