Drift into Failure, by Sidney Dekker. Studies failure analysis in complex systems, and basically argues that our classic reductionist/scientific method approach is the wrong way to study complex engineering failures.
How Buildings Learn, by Stewart Brand. This isn't about programming. It's about architecture, in the build-a-building sense. It studies what happens to buildings over the course of their lives, as opposed to just when they're first built.
Enterprise Integration Patterns, by Gregor Hohpe and Bobby Woolf. Learn how to use message queues and service busses correctly. Honestly, just read the first couple of chapters (65 pages or so), and the rest is reference, to look up as needed, so it's not as imposing as it sounds.
Advanced Programming in the UNIX Environment, by W. Richard Stevens. This book was my bible back in the olden days before http and ssh and stuff (I'm olde). Knowing how sockets really work can be an absolute lifesaver, even in this modern world of giant protocol stacks. Especially in this modern world.
The Art of Computer Programming, vols 1-3, by Donald Knuth. Only a madman would actually read them all, but they're good to have to remind you that there are mountains you can't even begin to climb.
A Deepness in the Sky, by Vernor Vinge. A science fiction novel that is really about hacking, set thousands of years in the future, when Moore's Law is long defeated and programmers are basically archeologists.
Design Patterns (aka Gang of Four), by Gamma/Helm/Johnson/Vlissides. There are lots of good books on design patterns, but you should really read the one that started it all. (For extra credit, read A Pattern Language, by Christopher Alexander - a book about urban architecture that inspired it.)
Continuous Delivery, by Jez Humble and David Farley. Stop thinking about your program in isolation, and learn how to deploy effectively!
Influence: The Psychology of Persuasion, by Robert Cialdini. This is DHH's favorite book. Learn how people think, and how to use that to design better products.
How to Win Friends and Influence People, by Dale Carnegie. Not creepy at all, despite how the title sounds in today's language. This book is the bible of how to get along with others. It's been in continuous print since before WWII, for good reason.
The Lean Startup, by Eric Ries. The best work you do is the work you find you don't need to do. Learn how to fail fast and save time on projects and product development, by building what customers want rather than what you think they need.