Echopraxia is great. I never understood those who thought it was disappointing. Blindsight is wonderful, but Echopraxia is possibly the more inventive one. It certainly pulls the narrative in a different direction.

I also really, really recommend The Freeze-Frame Revolution. It's about the crew on an starship trying to stop the rogue (sort of) AI that runs everything, the twist being that the crew is constantly under surveillance and must periodically hibernate in shifts for months or years at a time. It's a novella plus a handful of short stories set before and after the novel (all available for free on Peter Watts' website). Be warned, it's one bleak, dark universe.

Also, don't miss out on "The Colonel" (also on his website), a standalone short story that also happens to be a direct sequel to Blindsight.