Judea Pearl - Causality
John Earman - World Enough and Space-Time: Absolute vs. Relational Theories of Space and Time
James Woodward - Making Things Happen
Jeff Bub - Interpreting the Quantum World
Peter Godfrey-Smith - Darwinian Populations and Natural Selection
Jesse Prinz - The Conscious Brain
Kim Sterelny - Thought in a Hostile World
And some historically important works:
Carnap - The Logical Structure of the World (in a loose sense, the first attempt at an AI program)
Popper - The Logic of Scientific Discovery (the philosophy of science practicing scientists now inherit and unquestionably assume)
Kuhn - The Structure of Scientific Revolutions (a ubiquitous work on scientific practice)
Readers of HN might also dig up Scott Aaronson's paper on how complexity theory might be applied to certain philosophical questions.