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The best one is Prague Pictures by John Banville. It isn't so much a travel guide or a history book as it is the authors reflections on the city, his "handful of recollections, variations on a theme." The writing is beautiful and evocative, giving you a good feel for the atmosphere of the city itself. He throws in some historical tidbits to add depth and color, and gives tips on must-see places as it fits his narrative, but he mostly provides texture and feeling.
For practical purposes, I love my Eyewitness Travel Guide for Prague. I've been trying to figure out a plan for my free time in Prague...which areas of the city look the most interesting, which museums, etc.