2001: A Space Odyssey still holds up incredibly well. A true classic of the genre that not even the equally great Kubrick adaptation could fully capture.

John Scalzi's other books are pretty great too. Check out The Interdependency Series. It's about an interstellar empire that can only navigate through wormholes that are now closing up. The last emperor foresaw this and is trying to save as many humans as possible while fending off political rivals and assassins.

For a similar series check out Foundation from Isaac Asimov. It's more of an anthology of stories over the course of a millennium but Asimov has a brilliant way of piecing the story together through the vast gaps in time.

Hyperion is an honorable mention. It's another anthology told a la Canterbury Tales revolving around a mysterious and invincible metallic monster known as a Shrike, which is known to impale its victims in a metal tree - dooming them to an eternity of agony in a pocket dimension.