An Introduction General Relativity, Spacetime and Geometry by Carol
General Relativity by Wald
Gravitation by Misner Thorne and Wheeler
Mathematical Methods for Physics by Afken and Weber
Fundamentals of Interferometric Gravitational Wave Detectors by Saulson (1994)
Computational Physics by Newman
Nodal Discontinuous Galerkin Methods by Hesthaven and Warburton
Numerical Recipes in C, C++, and FORTRAN by Teukolsky, Vetterling, and Flannery
Table of Integrals, Series, and Products by Gradshtyn and Rzybik
Data Reduction and Error Analysis for the Physical Sciences by Bevington and Robinson
C++ by Rao
An Introduction to Quantum Field Theory by Peskin and Schroeder
Cosmology by Weinberg
Principles of Quantum Mechanics by Shankar
Classical Electrodynamics by Jackson
Classical Mechanics by Goldstein Poole and Safko
Modern Quantum Mechanics by Sakurai
Modern Cosmology by Dodelson
Galactic Dynamics by Binney and Tremaine
Advanced Quantum Mechanics by Scwhabl
Cosmology, Barbara Ryden (lecture notes)
Physics of Neutrinos by Fukugita and Yanigida
Mathematical Statistics by Larsen and Marx
Statistics for Nuclear and Particle Physicists
Concepts, Probability, and Stochastic Modelling by Higgins and Keller-McNulty
Elements of Statistical Learning Data Mining Inference and Prediction by Hastie Tibshirani and Friedman (I'm definitely half way through...)
Data Analysis, a Bayesian Tutorial by Sivia (definitely part way through this one as well)
Active Galactic Nucleii by Krolic
Radiative Processes in Astrophysics by Rybiki and Lightman
Statistical Mechanics by Schwabl (maybe)
Java for everyone by Horstmann (why did I take Java?)
Black Holes and Time Warps by Thorne
The First Three Minutes by Weinberg
Brief History of Time by Tyson
The Inflationary Universe by Guth
Exploring Black Holes by Taylor and Wheeler
Griffiths for quantum and E&M but I no longer own either
I'm missing a HUGE number of more current pop science or introductory specialized science references on this list, many of which are from authors who are friends. My appologies!