Great suggestions! However, any discussion of Greg Egan is not complete without "Diaspora"! A novel about a world where most humans' minds have been scanned into a benevolent, human-operated machine world like The Matrix. Best book about those concepts I've ever read.
It explores (with an intriguing plot) questions like, "What do you do with yourself when you control the matrix and, furthermore, can rewrite the code that is your own mind?"
"How do senses and perception work in a digital world lacking all physical constraints? In what kind of environment will people interact? Will they have physics-simulated bodies or just be abstract shapes?"
"How does the nature of space exploration change if you can slow down your mind until the orbit of planets is your day/night cycle?" It goes after these questions in a believable hard science fiction way. The remaining normal humans meanwhile see those living in the machine world as a deception or trick of evil robots, causing the digital humans great anguish since they wish to relieve the others of their pain and suffering. Beautiful and mind-bending.
PERMUTATION CITY http://amzn.com/1597805394
And here's some ultrasharp online science fiction
RA, FINE STRUCTURE, CAUSAL NOOSE ETC http://qntm.org/fiction
FRIENDSHIP IS OPTIMAL http://www.fimfiction.net/story/62074/friendship-is-optimal